Closed
Description
Thanks for preparing this great tools for long read sequences analysis. I have a problem with running the test sample for type sc. When I run it like the below in command line , I get the following error:
(base) bash-4.4$ nextflow run -profile local -params-file params-local-sc.json main.nf
Nextflow 24.10.4 is available - Please consider updating your version to it
N E X T F L O W ~ version 24.10.0
Launching `main.nf` [scruffy_bose] DSL2 - revision: b6c65d670c
executor > local (2)
[20/5720e6] laava:map_reads (1) | 1 of 1 ✔
[2b/001117] laava:make_report (1) | 0 of 1
ERROR ~ Error executing process > 'laava:make_report (1)'
Caused by:
Process `laava:make_report (1)` terminated with an error exit status (1)
Command executed:
write_sample_metadata.py "sc.subsample005" "sc.subsample005" "sc.subsample005.sort_by_name.sam" \
-o "sc.subsample005.metadata.tsv"
prepare_annotation.py "sc.annotation.bed" "sc.subsample005.reference_names.tsv" \
"ITR-L" "ITR-R" \
-o annotation.txt
make_report.sh \
"sc.subsample005" \
sc \
200 \
100 \
100 \
"sc.subsample005.sort_by_name.sam" \
annotation.txt \
"" \
""
Command exit status:
1
Command output:
total 60K
-rw-------. 1 root root 0 Jan 30 19:56 .command.begin
-rw-------. 1 root root 748 Jan 30 19:56 .command.err
-rw-------. 1 root root 748 Jan 30 19:56 .command.log
-rw-------. 1 root root 0 Jan 30 19:56 .command.out
-rw-------. 1 root root 11K Jan 30 19:56 .command.run
-rw-------. 1 root root 436 Jan 30 19:56 .command.sh
-rw-r--r--. 1 root root 0 Jan 30 19:56 .command.trace
lrwxrwxrwx. 1 root root 34 Jan 30 19:56 NO_FILE -> /c/laava-main/bin/NO_FILE
-rw-r--r--. 1 root root 215 Jan 30 19:56 annotation.txt
lrwxrwxrwx. 1 root root 53 Jan 30 19:56 sc.annotation.bed -> /c/laava-main/test/samples/sc.annotation.bed
-rw-r--r--. 1 root root 111 Jan 30 19:56 sc.subsample005.metadata.tsv
lrwxrwxrwx. 1 root root 114 Jan 30 19:56 sc.subsample005.reference_names.tsv -> /c/laava-main/workflow-outputs/work/20/5720e620643e4ae0bd939d25c3c2c8/sc.subsample005.reference_names.tsv
lrwxrwxrwx. 1 root root 111 Jan 30 19:56 sc.subsample005.sort_by_name.sam -> /c/laava-main/workflow-outputs/work/20/5720e620643e4ae0bd939d25c3c2c8/sc.subsample005.sort_by_name.sam
Reads sc.subsample005.sort_by_name.sam appear to be in SAM format
Starting summarize_alignment
Command error:
Going from 972 to 990
Going from 990 to 1008
Going from 1008 to 1026
Going from 1026 to 1044
Going from 1044 to 1062
Going from 1062 to 1080
Going from 1080 to 1098
Going from 1098 to 1116
Going from 1116 to 1134
Going from 1134 to 1152
Going from 1152 to 1170
Going from 1170 to 1188
Going from 1188 to 1206
Going from 1206 to 1224
Going from 1224 to 1242
Going from 1242 to 1260
Going from 1260 to 1278
Going from 1278 to 1296
Going from 1296 to 1314
Going from 1314 to 1332
Going from 1332 to 1350
Going from 1350 to 1368
Going from 1368 to 1386
Going from 1386 to 1404
Going from 1404 to 1422
Going from 1422 to 1440
Going from 1440 to 1458
Going from 1458 to 1476
Going from 1476 to 1494
Going from 1494 to 1512
executor > local (2)
[20/5720e6] laava:map_reads (1) | 1 of 1 ✔
[2b/001117] laava:make_report (1) | 1 of 1, failed: 1 ✘
ERROR ~ Error executing process > 'laava:make_report (1)'
Caused by:
Process `laava:make_report (1)` terminated with an error exit status (1)
Command executed:
write_sample_metadata.py "sc.subsample005" "sc.subsample005" "sc.subsample005.sort_by_name.sam" \
-o "sc.subsample005.metadata.tsv"
prepare_annotation.py "sc.annotation.bed" "sc.subsample005.reference_names.tsv" \
"ITR-L" "ITR-R" \
-o annotation.txt
make_report.sh \
"sc.subsample005" \
sc \
200 \
100 \
100 \
"sc.subsample005.sort_by_name.sam" \
annotation.txt \
"" \
""
Command exit status: 1
Command output:
total 60K
-rw-------. 1 root root 0 Jan 30 19:56 .command.begin
-rw-------. 1 root root 748 Jan 30 19:56 .command.err
-rw-------. 1 root root 748 Jan 30 19:56 .command.log
-rw-------. 1 root root 0 Jan 30 19:56 .command.out
-rw-------. 1 root root 11K Jan 30 19:56 .command.run
-rw-------. 1 root root 436 Jan 30 19:56 .command.sh
-rw-r--r--. 1 root root 0 Jan 30 19:56 .command.trace
lrwxrwxrwx. 1 root root 34 Jan 30 19:56 NO_FILE -> /c/laava-main/bin/NO_FILE
-rw-r--r--. 1 root root 215 Jan 30 19:56 annotation.txt
lrwxrwxrwx. 1 root root 53 Jan 30 19:56 sc.annotation.bed -> /c/laava-main/test/samples/sc.annotation.bed
-rw-r--r--. 1 root root 111 Jan 30 19:56 sc.subsample005.metadata.tsv
lrwxrwxrwx. 1 root root 114 Jan 30 19:56 sc.subsample005.reference_names.tsv -> /c/laava-main/workflow-outputs/work/20/5720e620643e4ae0bd939d25c3c2c8/sc.subsample005.reference_names.tsv
lrwxrwxrwx. 1 root root 111 Jan 30 19:56 sc.subsample005.sort_by_name.sam -> /c/laava-main/workflow-outputs/work/20/5720e620643e4ae0bd939d25c3c2c8/sc.subsample005.sort_by_name.sam
Reads sc.subsample005.sort_by_name.sam appear to be in SAM format
Starting summarize_alignment
Command error:
Going from 972 to 990
Going from 990 to 1008
Going from 1008 to 1026
Going from 1026 to 1044
Going from 1044 to 1062
Going from 1062 to 1080
Going from 1080 to 1098
Going from 1098 to 1116
Going from 1116 to 1134
Going from 1134 to 1152
Going from 1152 to 1170
Going from 1170 to 1188
Going from 1188 to 1206
Going from 1206 to 1224
Going from 1224 to 1242
Going from 1242 to 1260
Going from 1260 to 1278
Going from 1278 to 1296
Going from 1296 to 1314
Going from 1314 to 1332
Going from 1332 to 1350
Going from 1350 to 1368
Going from 1368 to 1386
Going from 1386 to 1404
Going from 1404 to 1422
Going from 1422 to 1440
Going from 1440 to 1458
Going from 1458 to 1476
Going from 1476 to 1494
Going from 1494 to 1512
Going from 1512 to 1530
Going from 1530 to 1548
Going from 1548 to 1566
Going from 1566 to 1584
Going from 1584 to 1602
Going from 1602 to 1620
Going from 1620 to 1638
Going from 1638 to 1656
Going from 1656 to 1674
Going from 1674 to 1692
Traceback (most recent call last):
File "/opt/laava/summarize_alignment.py", line 978, in <module>
main(args)
File "/opt/laava/summarize_alignment.py", line 829, in main
per_read_tsv, full_out_bam = run_processing_parallel(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/laava/summarize_alignment.py", line 733, in run_processing_parallel
starting_readname = readname_list[i * chunk_size]
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
IndexError: list index out of range
Work dir:
/c/laava-main/workflow-outputs/work/2b/00111713d5f3b1c715bd44baa7e109
Container:
ghcr.io/formbio/laava:dev
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '.nextflow.log' file for details
but running ss one works fine:
(base) bash-4.4$ nextflow run -profile local -params-file params-local-ss.json main.nf
Nextflow 24.10.4 is available - Please consider updating your version to it
N E X T F L O W ~ version 24.10.0
Launching `main.nf` [distraught_leakey] DSL2 - revision: b6c65d670c
executor > local (2)
[64/67c137] laava:map_reads (1) | 1 of 1 ✔
[ae/38db23] laava:make_report (1) | 1 of 1 ✔
Completed at: 30-Jan-2025 15:01:12
Duration : 1m 18s
CPU hours : (a few seconds)
Succeeded : 2
(base) bash-4.4$
I realized that it comes from here
and if I change it to
chunk_size = (total_num_reads // num_chunks)
and then run it locally like this
./make_report.sh sc.subsample005 sc 200 100 100 output/alignment/sc.subsample005.sort_by_name.sam sc.annotation.txt
it passes this step successfully! But I don't want to run it locally. Can you please help with this? Thanks