miga-base 0.7.24.0 → 0.7.26.0

data/utils/enveomics/Pipelines/assembly.pbs/stats.pbs

@@ -1,57 +0,0 @@
-#!/bin/bash
-#PBS -q iw-shared-6
-#PBS -l nodes=1:ppn=1
-#PBS -l mem=1gb
-#PBS -l walltime=3:00:00
-#PBS -k oe
-
-# Check mandatory variables
-if [[ "$LIB" == "" ]]; then
-   echo "Error: LIB is mandatory" >&2
-   exit 1;
-fi
-if [[ "$PDIR" == "" ]]; then
-   echo "Error: PDIR is mandatory" >&2
-   exit 1;
-fi
-
-# Run
-module load perl/5.14.4
-echo "K N50 used reads " > $LIB.velvet.n50
-echo "K N50 used reads " > $LIB.soap.n50
-for ID in $(seq 10 31); do
-   let KMER=$ID*2+1
-   DIRV="$LIB.velvet_$KMER"
-   DIRS="$LIB.soap_$KMER"
-   echo $KMER > $LIB.velvet.n50.$KMER
-   echo $KMER > $LIB.soap.n50.$KMER
-   # N50 (>=500)
-   perl "$PDIR/FastA.N50.pl" "$DIRV/contigs.fa" 500 | grep '^N50' | sed -e 's/.*: //' >> $LIB.velvet.n50.$KMER
-   perl "$PDIR/FastA.N50.pl" "$DIRS/O.contig" 500 | grep '^N50' | sed -e 's/.*: //' >> $LIB.soap.n50.$KMER
-   # Used and Total reads
-   tail -n 1 $DIRV/Log | sed -e 's/.* using \\([0-9]*\\)\\/\\([0-9]*\\) reads.*/\\1\\n\\2/' >> $LIB.velvet.n50.$KMER
-   if [ -e "$DIRS/O.readOnContig" ] ; then
-      cat "$DIRS/O.readOnContig" | grep -vc '^read' >> $LIB.soap.n50.$KMER
-   elif [ -e "$DIRS/O.readOnContig.gz" ] ; then
-      zcat "$DIRS/O.readOnContig.gz" | grep -vc '^read' >> $LIB.soap.n50.$KMER
-   else
-      echo 0 >> $LIB.soap.n50.$KMER
-   fi
-   head -n 1 $DIRS/O.peGrads | awk '{print $3}' >> $LIB.soap.n50.$KMER
-   # Join
-   (cat $LIB.velvet.n50.$KMER | tr "\\n" " "; echo) >> $LIB.velvet.n50
-   rm $LIB.velvet.n50.$KMER
-   (cat $LIB.soap.n50.$KMER | tr "\\n" " "; echo) >> $LIB.soap.n50
-   rm $LIB.soap.n50.$KMER
-done
-
-# Create plot
-module load R/3.1.2
-echo "
-source('$PDIR/kSelector.R');
-pdf('$LIB.n50.pdf', 13, 7);
-kSelector('$LIB.velvet.n50', '$LIB (Velvet)');
-kSelector('$LIB.soap.n50', '$LIB (SOAP)');
-dev.off();
-" | R --vanilla -q
-

data/utils/enveomics/Pipelines/assembly.pbs/velvet.pbs

@@ -1,63 +0,0 @@
-#!/bin/bash
-#PBS -l nodes=1:ppn=1
-#PBS -k oe
-
-# Some defaults for the parameters
-FORMAT=${FORMAT:-fasta};
-INSLEN=${INSLEN:-300};
-USECOUPLED=${USECOUPLED:-yes};
-USESINGLE=${USESINGLE:-no};
-CLEANUP=${CLEANUP:-yes}
-
-# Check mandatory variables
-if [[ "$LIB" == "" ]]; then
-   echo "Error: LIB is mandatory" >&2
-   exit 1;
-fi
-if [[ "$PDIR" == "" ]]; then
-   echo "Error: PDIR is mandatory" >&2
-   exit 1;
-fi
-if [[ "$DATA" == "" ]]; then
-   echo "Error: DATA is mandatory" >&2
-   exit 1;
-fi
-
-# Prepare input
-KMER=$PBS_ARRAYID
-CWD=$(pwd)
-DIR="$CWD/$LIB.velvet_$KMER"
-
-# Run
-module load velvet/1.2.10
-echo velveth > $DIR.proc
-CMD="velveth_101_omp $DIR $KMER -$FORMAT"
-if [[ "$USECOUPLED" == "yes" ]]; then
-   CMD="$CMD -shortPaired $DATA/$LIB.CoupledReads.fa"
-fi
-if [[ "$USESINGLE" == "yes" ]]; then
-   CMD="$CMD -short $DATA/$LIB.SingleReads.fa"
-fi
-if [[ "$VELVETH_EXTRA" != "" ]]; then
-   CMD="$CMD $VELVETH_EXTRA"
-fi
-$CMD &> $DIR.hlog
-echo velvetg > $DIR.proc
-velvetg_101_omp "$DIR" -exp_cov auto -cov_cutoff auto -ins_length "$INSLEN" $VELVETG_EXTRA &> $DIR.glog
-if [[ -d $DIR ]] ; then
-   if [[ -s $DIR/contigs.fa ]] ; then
-      if [[ "$CLEANUP" != "no" ]] ; then
-	 echo cleanup > $DIR.proc
-	 rm $DIR/Sequences
-	 rm $DIR/Roadmaps
-	 rm $DIR/*Graph*
-      fi
-      echo done > $DIR.proc
-   else
-      echo "$0: Error: File $DIR/contigs.fa doesn't exist, something went wrong" >&2
-      exit 1
-   fi
-else
-   echo "$0: Error: Directory $DIR doesn't exist, something went wrong" >&2
-   exit 1
-fi

data/utils/enveomics/Pipelines/blast.pbs/01.pbs.bash

@@ -1,38 +0,0 @@
-# blast.pbs pipeline
-# Step 01 : Initialize input files
-
-# 00. Read configuration
-cd $SCRATCH ;
-TASK="dry" ;
-source "$PDIR/RUNME.bash" ;
-echo "$PBS_JOBID" > "$SCRATCH/success/01.00" ;
-
-if [[ ! -e "$SCRATCH/success/01.01" ]] ; then
-   # 01. BEGIN
-   REGISTER_JOB "01" "01" "Custom BEGIN function" \
-      && BEGIN \
-      || exit 1 ;
-   touch "$SCRATCH/success/01.01" ;
-fi
-
-if [[ ! -e "$SCRATCH/success/01.02" ]] ; then
-   # 02. Split
-   [[ -d "$SCRATCH/tmp/split" ]] && rm -R "$SCRATCH/tmp/split" ;
-   REGISTER_JOB "01" "02" "Splitting query files" \
-      && mkdir "$SCRATCH/tmp/split" \
-      && perl "$PDIR/FastA.split.pl" "$INPUT" "$SCRATCH/tmp/split/$PROJ" "$MAX_JOBS" \
-      || exit 1 ;
-   touch "$SCRATCH/success/01.02" ;
-fi ;
-
-if [[ ! -e "$SCRATCH/success/01.03" ]] ; then
-   # 03. Finalize
-   REGISTER_JOB "01" "03" "Finalizing input preparation" \
-      && mv "$SCRATCH/tmp/split" "$SCRATCH/tmp/in" \
-      || exit 1 ;
-   touch "$SCRATCH/success/01.03" ;
-fi ;
-
-[[ -d "$SCRATCH/tmp/out" ]] || ( mkdir "$SCRATCH/tmp/out" || exit 1 ) ;
-JOB_DONE "01" ;
-

data/utils/enveomics/Pipelines/blast.pbs/02.pbs.bash

@@ -1,73 +0,0 @@
-# blast.pbs pipeline
-# Step 02 : Run BLAST
-
-# Read configuration
-cd $SCRATCH ;
-TASK="dry" ;
-source "$PDIR/RUNME.bash" ;
-
-# 00. Initial vars
-ID_N=$PBS_ARRAYID
-[[ "$ID_N" == "" ]] && exit 1 ;
-[[ -e "$SCRATCH/success/02.$ID_N" ]] && exit 0 ;
-IN="$SCRATCH/tmp/in/$PROJ.$ID_N.fa" ;
-OUT="$SCRATCH/tmp/out/$PROJ.blast.$ID_N" ;
-FINAL_OUT="$SCRATCH/results/$PROJ.$ID_N.blast" ;
-if [[ -e "$SCRATCH/success/02.$ID_N.00" ]] ; then
-   pre_job=$(cat "$SCRATCH/success/02.$ID_N.00") ;
-   state=$(qstat -f "$pre_job" 2>/dev/null | grep job_state | sed -e 's/.*= //')
-   if [[ "$state" == "R" ]] ; then
-      echo "Warning: This task is already being executed by $pre_job. Aborting." >&2 ;
-      exit 0 ;
-   elif [[ "$state" == "" ]] ; then
-      echo "Warning: This task was initialized by $pre_job, but it's currently not running. Superseding." >&2 ;
-   fi ;
-fi
-echo "$PBS_JOBID" > "$SCRATCH/success/02.$ID_N.00" ;
-
-# 01. Before BLAST
-if [[ ! -e "$SCRATCH/success/02.$ID_N.01" ]] ; then
-   BEFORE_BLAST "$IN" "$OUT" || exit 1 ;
-   touch "$SCRATCH/success/02.$ID_N.01" ;
-fi ;
-
-# 02. Run BLAST
-if [[ ! -e "$SCRATCH/success/02.$ID_N.02" ]] ; then
-   # Recover previous runs, if any
-   if [[ -s "$OUT" ]] ; then
-      perl "$PDIR/BlastTab.recover_job.pl" "$IN" "$OUT" \
-	 || exit 1 ;
-   fi ;
-   # Run BLAST
-   RUN_BLAST "$IN" "$OUT" \
-      && mv "$OUT" "$OUT-z" \
-      || exit 1 ;
-   touch "$SCRATCH/success/02.$ID_N.02" ;
-fi ;
-
-# 03. Collect BLAST parts
-if [[ ! -e "$SCRATCH/success/02.$ID_N.03" ]] ; then
-   if [[ -e "$OUT" ]] ; then
-      echo "Warning: The file $OUT pre-exists, but the BLAST collection was incomplete." >&2 ;
-      echo "  I'm assuming that it corresponds to the first part of the result, but you should check manually." >&2 ;
-      echo "  The last lines are:" >&2 ;
-      tail -n 3 "$OUT" >&2 ;
-   else
-      touch "$OUT" || exit 1 ;
-   fi ;
-   for i in $(ls $OUT-*) ; do
-      cat "$i" >> "$OUT" ;
-      rm "$i" || exit 1 ;
-   done ;
-   mv "$OUT" "$FINAL_OUT"
-   touch "$SCRATCH/success/02.$ID_N.03" ;
-fi ;
-
-# 04. After BLAST
-if [[ ! -e "$SCRATCH/success/02.$ID_N.04" ]] ; then
-   AFTER_BLAST "$IN" "$FINAL_OUT" || exit 1 ;
-   touch "$SCRATCH/success/02.$ID_N.04" ;
-fi ;
-
-touch "$SCRATCH/success/02.$ID_N" ;
-

data/utils/enveomics/Pipelines/blast.pbs/03.pbs.bash

@@ -1,21 +0,0 @@
-# blast.pbs pipeline
-# Step 03 : Finalize
-
-# Read configuration
-cd $SCRATCH ;
-TASK="dry" ;
-source "$PDIR/RUNME.bash" ;
-PREFIX="$SCRATCH/results/$PROJ" ;
-OUT="$SCRATCH/$PROJ.blast" ;
-echo "$PBS_JOBID" > "$SCRATCH/success/02.00" ;
-
-# 01. END
-if [[ ! -e "$SCRATCH/success/03.01" ]] ; then
-   REGISTER_JOB "03" "01" "Custom END function" \
-      && END "$PREFIX" "$OUT" \
-      || exit 1 ;
-   touch "$SCRATCH/success/03.01" ;
-fi ;
-
-JOB_DONE "03" ;
-

data/utils/enveomics/Pipelines/blast.pbs/BlastTab.recover_job.pl

@@ -1,72 +0,0 @@
-#!/usr/bin/perl
-
-use warnings;
-use strict;
-use File::Copy;
-
-my($fasta, $blast) = @ARGV;
-
-($fasta and $blast) or die "
-.USAGE:
-   $0 query.fa blast.txt
-
-   query.fa	Query sequences in FastA format.
-   blast.txt	Incomplete BLAST output in tabular format.
-
-";
-
-print "Fixing $blast:\n";
-my $blast_res;
-for(my $i=0; 1; $i++){
-   $blast_res = "$blast-$i";
-   last unless -e $blast_res;
-}
-open BLAST, "<", $blast or die "Cannot read the file: $blast: $!\n";
-open TMP, ">", "$blast-tmp" or die "Cannot create the file: $blast-tmp: $!\n";
-my $last="";
-my $last_id="";
-my $before = "";
-while(my $ln=<BLAST>){
-   chomp $ln;
-   last unless $ln =~ m/(.+?)\t/;
-   my $id = $1;
-   if($id eq $last_id){
-      $last.= $ln."\n";
-   }else{
-      print TMP $last if $last;
-      $before = $last_id;
-      $last = $ln."\n";
-      $last_id = $id;
-   }
-}
-close BLAST;
-close TMP;
-
-move "$blast-tmp", $blast_res or die "Cannot move file $blast-tmp into $blast_res: $!\n";
-unlink $blast or die "Cannot delete file: $blast: $!\n";
-
-unless($before eq ""){
-   print "[$before] ";
-   $before = ">$before";
-   
-   open FASTA, "<", $fasta or die "Cannot read file: $fasta: $!\n";
-   open TMP, ">", "$fasta-tmp" or die "Cannot create file: $fasta-tmp: $!\n";
-   my $print = 0;
-   my $at = 0;
-   my $i = 0;
-   while(my $ln=<FASTA>){
-      $i++;
-      $print = 1 if $at and $ln =~ /^>/;
-      print TMP $ln if $print;
-      $ln =~ s/\s+.*//;
-      chomp $ln;
-      $at = $i if $ln eq $before;
-   }
-   close TMP;
-   close FASTA;
-   printf 'recovered at %.2f%% (%d/%d).'."\n", 100*$at/$i, $at, $i if $i;
-
-   move $fasta, "$fasta.old" or die "Cannot move file $fasta into $fasta.old: $!\n";
-   move "$fasta-tmp", $fasta or die "Cannot move file $fasta-tmp into $fasta: $!\n";
-}
-

data/utils/enveomics/Pipelines/blast.pbs/CONFIG.mock.bash

@@ -1,98 +0,0 @@
-#!/bin/bash
-
-##################### VARIABLES
-# Queue and resources.
-QUEUE="iw-shared-6" ;
-MAX_JOBS=500 ; # Maximum number of concurrent jobs. Never exceed 1990.
-PPN=2 ;
-RAM="9gb" ;
-
-# Paths
-SCRATCH_DIR="$HOME/scratch/pipelines/blast" ; # Where the outputs and temporals will be created
-INPUT="$HOME/data/my-large-file.fasta" ; # Input query file
-DB="$HOME/data/db/nr" ; # Input database
-PROGRAM="blastp" ;
-
-# Pipeline
-MAX_TRIALS=5 ; # Maximum number of automated attempts to re-start a job
-
-##################### FUNCTIONS
-## All the functions below can be edited to suit your particular job.
-## No function can be empty, but you can use a "dummy" function (like true).
-## All functions have access to any of the variables defined above.
-## 
-## The functions are executed in the following order (from left to right):
-##
-##           / -----> BEFORE_BLAST --> RUN_BLAST --> AFTER_BLAST ---\
-##          /              ···            ···            ···         \
-## BEGIN --#--------> BEFORE_BLAST --> RUN_BLAST --> AFTER_BLAST -----#---> END
-##          \              ···            ···            ···         /
-##           \ -----> BEFORE_BLAST --> RUN_BLAST --> AFTER_BLAST ---/
-##
-
-# Function to execute ONLY ONCE at the begining
-function BEGIN {
-   ### Format the database (assuming proteins, check commands):
-   # module load ncbi_blast/2.2.25 || exit 1 ;
-   # makeblastdb -in $HOME/data/some-database.faa -title $DB -dbtype prot || exit 1 ;
-   # module unload ncbi_blast/2.2.25 || exit 1 ;
-   ### Don't do anything:
-   true ;
-}
-
-# Function to execute BEFORE running the BLAST, for each sub-task.
-function BEFORE_BLAST {
-   local IN=$1 # Query file
-   local OUT=$2 # Blast file (to be created)
-   ### Don't do anything:
-   true ;
-}
-
-# Function that executes BLAST, for each sub-task
-function RUN_BLAST {
-   local IN=$1 # Query file
-   local OUT=$2 # Blast file (to be created)
-   ### Run BLAST+ with 13th and 14th columns (query length and subject length):
-   module load ncbi_blast/2.2.28_binary || exit 1 ;
-   $PROGRAM -query $IN -db $DB -out $OUT -num_threads $PPN \
-   	-outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen" \
-	|| exit 1 ;
-   module unload ncbi_blast/2.2.28_binary || exit 1 ;
-   ### Run BLAT (nucleotides)
-   # module load blat/rhel6 || exit 1 ;
-   # blat $DB $IN -out=blast8 $OUT || exit 1 ;
-   # module unload blat/rhel6 || exit 1 ;
-   ### Run BLAT (proteins)
-   # module load blat/rhel6 || exit 1 ;
-   # blat $DB $IN -out=blast8 -prot $OUT || exit 1 ;
-   # module unload blat/rhel6 || exit 1 ;
-}
-
-# Function to execute AFTER running the BLAST, for each sub-task
-function AFTER_BLAST {
-   local IN=$1 # Query files
-   local OUT=$2 # Blast files
-   ### Filter by best-match:
-   # sort $OUT | perl $PDIR/../../Scripts/BlastTab.best_hit_sorted.pl > $OUT.bm
-   ### Filter by Bit-score 60:
-   # awk '$12>=60' $OUT > $OUT.bs60
-   ### Filter by corrected identity 95 (only if it has the additional 13th column):
-   # awk '$3*$4/$13 >= 95' $OUT > $OUT.ci95
-   ### Don't do anything:
-   true ;
-}
-
-# Function to execute ONLY ONCE at the end, to concatenate the results
-function END {
-   local PREFIX=$1 # Prefix of all Blast files
-   local OUT=$2 # Single Blast output (to be created).
-   ### Simply concatenate files:
-   # cat $PREFIX.*.blast > $OUT
-   ### Concatenate only the filtered files (if filtering in AFTER_BLAST):
-   # cat $PREFIX.*.blast.bs60 > $OUT
-   ### Sort the BLAST by query (might require considerable RAM):
-   # sort -k 1 $PREFIX.*.blast > $OUT
-   ### Don't do anyhthing:
-   true ;
-}
-

data/utils/enveomics/Pipelines/blast.pbs/FastA.split.pl

@@ -1 +0,0 @@
-../../Scripts/FastA.split.pl

data/utils/enveomics/Pipelines/blast.pbs/README.md

@@ -1,127 +0,0 @@
-@author: Luis Miguel Rodriguez-R <lmrodriguezr at gmail dot com>
-
-@update: Feb-20-2014
-
-@license: artistic 2.0
-
-@status: auto
-
-@pbs: yes
-
-# IMPORTANT
-
-This pipeline was developed for the [PACE cluster](http://pace.gatech.edu/).  You
-are free to use it in other platforms with adequate adjustments.
-
-# PURPOSE
-
-Simplifies submitting and tracking large BLAST jobs in cluster.
-
-# HELP
-
-1. Files preparation:
-
-   1.1. Obtain the enveomics package in the cluster. You can use: `git clone https://github.com/lmrodriguezr/enveomics.git`
-   
-   1.2. Prepare the query sequences and the database.
-   
-   1.3. Copy the file `CONFIG.mock.bash` to `CONFIG.<name>.bash`, where `<name>` is a
-      short name for your project (avoid characters other than alphanumeric).
-   
-   1.4. Change the variables in `CONFIG.<name>.bash`. The **Queue and resources** and the
-      **Pipeline** variables are very standard, and can be kept unchanged. The **Paths**
-      variables indicate where your input files are and where the output files are to
-      be created, so check them carefully. Finally, the **FUNCTIONS** define the core
-      functionality of the pipeline, and should also be reviewed. By default, the
-      Pipeline simply runs BLAST+, with default parameters and tabular output with two
-      extra columns (qlen and slen). However, additional functionality can easily be
-      incorporated via these functions, such as BLAST filtering, concatenation, sorting,
-      or even execution of other programs instead of BLAST, such as BLAT, etc. Note that
-      the output MUST be BLAST-like tabular, because this is the only format supported
-      to check completeness and recover incomplete runs.
-   
-2. Pipeline execution:
-   
-   2.1. To initialize a run, execute: `./RUNME.bash <name> run`.
-
-   2.2. To check the status of a job, execute: `./RUNME.bash <name> check`.
-
-   2.3. To pause a run, execute: `./RUNME.bash <name> pause` (see 2.1 to resume).
-
-   2.4. To check if your CONFIG defines all required parameters, execute: `./RUNME.bash <name> dry`.
-
-   2.5. To review all the e/o files in the run, execute: `./RUNME.bash <name> eo`.
-
-3. Finalizing:
-   
-   3.1. `./RUNME.bash <name> check` will inform you if a project finished. If it finished successfully,
-      you can review your (split) results in $SCRATCH/results. If you concatenated the results in the
-      `END` function, you should have a file with all the results in $SCRATCH/<name>.blast.
-
-   3.2. Usually, checking the e/o files at the end is a good idea (`./RUNME.bash <name> eo`). However,
-      bear in mind that this Pipeline can overcome several errors and is robust to most failures, so
-      don't be alarmed at the first sight of errors.
-
-# Comments
-
-* Some scripts contained in this package are actually symlinks to files in the
-  _Scripts_ folder.  Check the existance of these files when copied to
-  the cluster.
-
-# Troubleshooting
-
-1. Do I really have to change directory (`cd`) to the pipeline's folder everytime I want to execute
-   something?
-   
-   No.  Not really.  For simplicity, this file tells you to execute `./RUNME.bash`.  However, you don't
-   really have to be there, you can execute it from any location.  For example, if you saved enveomics in
-   your home directory, you can just execute `~/enveomics/blast.pbs/RUNME.bash` insted from any location
-   in the head node.
-
-2. When I check a project, few sub-jobs are Active for much longer than the others. How do I know if those
-   sub-jobs are really active?
-   
-   Lets review an example of a problematic run. When you run `./RUNME.bash <name> check`, you see the
-   following in the "Active jobs" section:
-   ````
-   Idle: 155829.shared-sched.pace.gatech.edu: 02: 00: Mon Mar 17 14:10:28 EDT 2014
-     Sub-jobs:500 Active:4 ( 0.8% ) Eligible:0 ( 0.0% ) Blocked:0 ( 0.0% ) Completed:496 ( 99.2% ) 
-   Idle: 155830.shared-sched.pace.gatech.edu: 02: 00: Mon Mar 17 14:10:28 EDT 2014
-   
-   Running jobs: 0.
-   Idle jobs: 2.
-   ````
-   That means that the job "155829.shared-sched.pace.gatech.edu" has four Active jobs, while all the others are Completed. This is
-   a sign of something problematic.  You can see the complete status of each array using
-   `checkjob -v <JOB_NAME>`. In our example above, you would run `checkjob -v 155829`. In the output
-   of checkjob, most jobs should report "Completed". In this example, there are four jobs that are not
-   complete:
-   ````
-   ...
-   387 : 155829[387] : Completed
-   388 : 155829[388] : Running
-   389 : 155829[389] : Running
-   390 : 155829[390] : Running
-   391 : 155829[391] : Running
-   392 : 155829[392] : Completed
-   ...
-   ````
-   So you can simply check these sub-jobs in more detail. For example, if I run `checkjob -v 155829[388]`,
-   I see that the job is running in the machine `iw-k30-12.pace.gatech.edu` (Task Distribution), so I can try
-   to login to that machine to check if the job is actually running, using `top -u $(whoami)`. However, when
-   I run `ssh iw-k30-12`, I got a "Connection closed" error, which means that the machine hung up. At this point,
-   you might want to try one of the following solutions:
-
-   2.1. Pause the project using `./RUNME.bash <name> pause`, wait a few minutes, and resume using
-        `./RUNME.bash <name> run`. If you tried this a couple of times and you still have sub-jobs hanging, try:
-   
-   2.2. Check if your sub-jobs finished. Sometimes sub-jobs die too soon to return a success code, but they actually
-        finished. Just run the following command: `ls <SCRATCH>/<name>/success/02.* | wc -l`, where `<SCRATCH>` is the
-	value you set for the `SCRATCH` variable in the CONFIG file, and `<name>` is the name of your project. If the
-	output of that command is a number, and that number is exactly six times the number of jobs (`MAX_JOBS` in the
-	CONFIG file, typically 500), then your step 2 actually finished. In my case, I have 500 jobs, and the output
-	was 3000, so my job finished successfully, but the pipeline didn't notice. You can manually tell the pipeline
-	to go on running: `touch <SCRATCH>/<name>/success/02`, and pausing/resuming the project (see 2.1 above). If
-	the output is not the expected number (in my case, 3000, which is 6*500), DON'T RUN `touch`, just try the
-	solution 2.1 above once again.
-