Job ID = 10165775 SRX = SRX9120611 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 39221397 spots for SRR12638554/SRR12638554.sra Written 39221397 spots for SRR12638554/SRR12638554.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166085 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:34 39221397 reads; of these: 39221397 (100.00%) were unpaired; of these: 12066691 (30.77%) aligned 0 times 22322033 (56.91%) aligned exactly 1 time 4832673 (12.32%) aligned >1 times 69.23% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4979241 / 27154706 = 0.1834 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:03:46: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:03:46: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:03:51: 1000000 INFO @ Thu, 08 Oct 2020 20:03:56: 2000000 INFO @ Thu, 08 Oct 2020 20:04:02: 3000000 INFO @ Thu, 08 Oct 2020 20:04:07: 4000000 INFO @ Thu, 08 Oct 2020 20:04:13: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:04:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:04:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:18: 6000000 INFO @ Thu, 08 Oct 2020 20:04:22: 1000000 INFO @ Thu, 08 Oct 2020 20:04:25: 7000000 INFO @ Thu, 08 Oct 2020 20:04:28: 2000000 INFO @ Thu, 08 Oct 2020 20:04:31: 8000000 INFO @ Thu, 08 Oct 2020 20:04:34: 3000000 INFO @ Thu, 08 Oct 2020 20:04:37: 9000000 INFO @ Thu, 08 Oct 2020 20:04:41: 4000000 INFO @ Thu, 08 Oct 2020 20:04:43: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:04:46: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:46: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:47: 5000000 INFO @ Thu, 08 Oct 2020 20:04:50: 11000000 INFO @ Thu, 08 Oct 2020 20:04:53: 1000000 INFO @ Thu, 08 Oct 2020 20:04:54: 6000000 INFO @ Thu, 08 Oct 2020 20:04:57: 12000000 INFO @ Thu, 08 Oct 2020 20:05:00: 2000000 INFO @ Thu, 08 Oct 2020 20:05:01: 7000000 INFO @ Thu, 08 Oct 2020 20:05:04: 13000000 INFO @ Thu, 08 Oct 2020 20:05:07: 3000000 INFO @ Thu, 08 Oct 2020 20:05:08: 8000000 INFO @ Thu, 08 Oct 2020 20:05:11: 14000000 INFO @ Thu, 08 Oct 2020 20:05:14: 4000000 INFO @ Thu, 08 Oct 2020 20:05:15: 9000000 INFO @ Thu, 08 Oct 2020 20:05:18: 15000000 INFO @ Thu, 08 Oct 2020 20:05:22: 5000000 INFO @ Thu, 08 Oct 2020 20:05:22: 10000000 INFO @ Thu, 08 Oct 2020 20:05:25: 16000000 INFO @ Thu, 08 Oct 2020 20:05:29: 11000000 INFO @ Thu, 08 Oct 2020 20:05:29: 6000000 INFO @ Thu, 08 Oct 2020 20:05:32: 17000000 INFO @ Thu, 08 Oct 2020 20:05:36: 12000000 INFO @ Thu, 08 Oct 2020 20:05:36: 7000000 INFO @ Thu, 08 Oct 2020 20:05:39: 18000000 INFO @ Thu, 08 Oct 2020 20:05:43: 13000000 INFO @ Thu, 08 Oct 2020 20:05:44: 8000000 INFO @ Thu, 08 Oct 2020 20:05:46: 19000000 INFO @ Thu, 08 Oct 2020 20:05:50: 14000000 INFO @ Thu, 08 Oct 2020 20:05:51: 9000000 INFO @ Thu, 08 Oct 2020 20:05:53: 20000000 INFO @ Thu, 08 Oct 2020 20:05:57: 15000000 INFO @ Thu, 08 Oct 2020 20:05:59: 10000000 INFO @ Thu, 08 Oct 2020 20:06:00: 21000000 INFO @ Thu, 08 Oct 2020 20:06:04: 16000000 INFO @ Thu, 08 Oct 2020 20:06:06: 11000000 INFO @ Thu, 08 Oct 2020 20:06:07: 22000000 INFO @ Thu, 08 Oct 2020 20:06:08: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:08: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:08: #1 total tags in treatment: 22175465 INFO @ Thu, 08 Oct 2020 20:06:08: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:06:08: #1 tags after filtering in treatment: 22175465 INFO @ Thu, 08 Oct 2020 20:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:08: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:08: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:10: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 20:06:10: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:10: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:10: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:10: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:10: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:10: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:06:10: #2 alternative fragment length(s) may be 1,45 bps INFO @ Thu, 08 Oct 2020 20:06:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.05_model.r WARNING @ Thu, 08 Oct 2020 20:06:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:10: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Thu, 08 Oct 2020 20:06:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:06:10: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:11: 17000000 INFO @ Thu, 08 Oct 2020 20:06:14: 12000000 INFO @ Thu, 08 Oct 2020 20:06:18: 18000000 INFO @ Thu, 08 Oct 2020 20:06:21: 13000000 INFO @ Thu, 08 Oct 2020 20:06:25: 19000000 INFO @ Thu, 08 Oct 2020 20:06:29: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:06:31: 20000000 INFO @ Thu, 08 Oct 2020 20:06:36: 15000000 INFO @ Thu, 08 Oct 2020 20:06:38: 21000000 INFO @ Thu, 08 Oct 2020 20:06:44: 16000000 INFO @ Thu, 08 Oct 2020 20:06:44: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:06:45: 22000000 INFO @ Thu, 08 Oct 2020 20:06:47: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:47: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:47: #1 total tags in treatment: 22175465 INFO @ Thu, 08 Oct 2020 20:06:47: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:06:47: #1 tags after filtering in treatment: 22175465 INFO @ Thu, 08 Oct 2020 20:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:47: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:47: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:48: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 20:06:48: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:48: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:48: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:48: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:48: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:48: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:06:48: #2 alternative fragment length(s) may be 1,45 bps INFO @ Thu, 08 Oct 2020 20:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.10_model.r WARNING @ Thu, 08 Oct 2020 20:06:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:48: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Thu, 08 Oct 2020 20:06:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:06:48: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:51: 17000000 INFO @ Thu, 08 Oct 2020 20:06:58: 18000000 INFO @ Thu, 08 Oct 2020 20:07:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.05_summits.bed INFO @ Thu, 08 Oct 2020 20:07:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:07:05: 19000000 INFO @ Thu, 08 Oct 2020 20:07:11: 20000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:07:18: 21000000 INFO @ Thu, 08 Oct 2020 20:07:22: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:25: 22000000 INFO @ Thu, 08 Oct 2020 20:07:26: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:26: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:26: #1 total tags in treatment: 22175465 INFO @ Thu, 08 Oct 2020 20:07:26: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:07:26: #1 tags after filtering in treatment: 22175465 INFO @ Thu, 08 Oct 2020 20:07:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:26: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:26: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:27: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 20:07:27: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Thu, 08 Oct 2020 20:07:27: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:27: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:27: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:27: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:27: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:07:27: #2 alternative fragment length(s) may be 1,45 bps INFO @ Thu, 08 Oct 2020 20:07:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.20_model.r WARNING @ Thu, 08 Oct 2020 20:07:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:07:27: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Thu, 08 Oct 2020 20:07:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:07:27: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.10_summits.bed INFO @ Thu, 08 Oct 2020 20:07:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:08:01: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:08:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:08:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:08:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120611/SRX9120611.20_summits.bed INFO @ Thu, 08 Oct 2020 20:08:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling