Job ID = 14160398 SRX = SRX8582554 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26159097 spots for SRR12054115/SRR12054115.sra Written 26159097 spots for SRR12054115/SRR12054115.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160531 ("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: 00:05:25 26159097 reads; of these: 26159097 (100.00%) were unpaired; of these: 528194 (2.02%) aligned 0 times 21218683 (81.11%) aligned exactly 1 time 4412220 (16.87%) aligned >1 times 97.98% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 5141179 / 25630903 = 0.2006 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.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, 09 Dec 2021 02:19:31: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:19:31: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:19:36: 1000000 INFO @ Thu, 09 Dec 2021 02:19:41: 2000000 INFO @ Thu, 09 Dec 2021 02:19:46: 3000000 INFO @ Thu, 09 Dec 2021 02:19:51: 4000000 INFO @ Thu, 09 Dec 2021 02:19:56: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:20:01: 6000000 INFO @ Thu, 09 Dec 2021 02:20:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.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, 09 Dec 2021 02:20:01: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:20:01: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:20:06: 7000000 INFO @ Thu, 09 Dec 2021 02:20:06: 1000000 INFO @ Thu, 09 Dec 2021 02:20:12: 8000000 INFO @ Thu, 09 Dec 2021 02:20:12: 2000000 INFO @ Thu, 09 Dec 2021 02:20:17: 9000000 INFO @ Thu, 09 Dec 2021 02:20:17: 3000000 INFO @ Thu, 09 Dec 2021 02:20:23: 10000000 INFO @ Thu, 09 Dec 2021 02:20:23: 4000000 INFO @ Thu, 09 Dec 2021 02:20:28: 11000000 INFO @ Thu, 09 Dec 2021 02:20:28: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.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, 09 Dec 2021 02:20:31: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:20:31: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:20:34: 12000000 INFO @ Thu, 09 Dec 2021 02:20:34: 6000000 INFO @ Thu, 09 Dec 2021 02:20:37: 1000000 INFO @ Thu, 09 Dec 2021 02:20:39: 13000000 INFO @ Thu, 09 Dec 2021 02:20:39: 7000000 INFO @ Thu, 09 Dec 2021 02:20:42: 2000000 INFO @ Thu, 09 Dec 2021 02:20:45: 14000000 INFO @ Thu, 09 Dec 2021 02:20:45: 8000000 INFO @ Thu, 09 Dec 2021 02:20:48: 3000000 INFO @ Thu, 09 Dec 2021 02:20:50: 15000000 INFO @ Thu, 09 Dec 2021 02:20:50: 9000000 INFO @ Thu, 09 Dec 2021 02:20:53: 4000000 INFO @ Thu, 09 Dec 2021 02:20:55: 16000000 INFO @ Thu, 09 Dec 2021 02:20:56: 10000000 INFO @ Thu, 09 Dec 2021 02:20:59: 5000000 INFO @ Thu, 09 Dec 2021 02:21:01: 17000000 INFO @ Thu, 09 Dec 2021 02:21:01: 11000000 INFO @ Thu, 09 Dec 2021 02:21:04: 6000000 INFO @ Thu, 09 Dec 2021 02:21:06: 18000000 INFO @ Thu, 09 Dec 2021 02:21:07: 12000000 INFO @ Thu, 09 Dec 2021 02:21:10: 7000000 INFO @ Thu, 09 Dec 2021 02:21:12: 19000000 INFO @ Thu, 09 Dec 2021 02:21:12: 13000000 INFO @ Thu, 09 Dec 2021 02:21:15: 8000000 INFO @ Thu, 09 Dec 2021 02:21:17: 20000000 INFO @ Thu, 09 Dec 2021 02:21:18: 14000000 INFO @ Thu, 09 Dec 2021 02:21:20: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:21:20: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:21:20: #1 total tags in treatment: 20489724 INFO @ Thu, 09 Dec 2021 02:21:20: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:21:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:21:20: #1 tags after filtering in treatment: 20489724 INFO @ Thu, 09 Dec 2021 02:21:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:21:20: #1 finished! INFO @ Thu, 09 Dec 2021 02:21:20: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:21:21: 9000000 INFO @ Thu, 09 Dec 2021 02:21:22: #2 number of paired peaks: 258 WARNING @ Thu, 09 Dec 2021 02:21:22: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Thu, 09 Dec 2021 02:21:22: start model_add_line... INFO @ Thu, 09 Dec 2021 02:21:22: start X-correlation... INFO @ Thu, 09 Dec 2021 02:21:22: end of X-cor INFO @ Thu, 09 Dec 2021 02:21:22: #2 finished! INFO @ Thu, 09 Dec 2021 02:21:22: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 02:21:22: #2 alternative fragment length(s) may be 1,45,531 bps INFO @ Thu, 09 Dec 2021 02:21:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.05_model.r WARNING @ Thu, 09 Dec 2021 02:21:22: #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, 09 Dec 2021 02:21:22: #2 You may need to consider one of the other alternative d(s): 1,45,531 WARNING @ Thu, 09 Dec 2021 02:21:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:21:22: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:21:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:21:24: 15000000 INFO @ Thu, 09 Dec 2021 02:21:27: 10000000 INFO @ Thu, 09 Dec 2021 02:21:29: 16000000 INFO @ Thu, 09 Dec 2021 02:21:32: 11000000 INFO @ Thu, 09 Dec 2021 02:21:35: 17000000 INFO @ Thu, 09 Dec 2021 02:21:38: 12000000 INFO @ Thu, 09 Dec 2021 02:21:40: 18000000 INFO @ Thu, 09 Dec 2021 02:21:43: 13000000 INFO @ Thu, 09 Dec 2021 02:21:46: 19000000 INFO @ Thu, 09 Dec 2021 02:21:49: 14000000 INFO @ Thu, 09 Dec 2021 02:21:51: 20000000 INFO @ Thu, 09 Dec 2021 02:21:52: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:21:55: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:21:55: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:21:55: #1 total tags in treatment: 20489724 INFO @ Thu, 09 Dec 2021 02:21:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:21:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:21:55: #1 tags after filtering in treatment: 20489724 INFO @ Thu, 09 Dec 2021 02:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:21:55: #1 finished! INFO @ Thu, 09 Dec 2021 02:21:55: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:21:57: #2 number of paired peaks: 258 WARNING @ Thu, 09 Dec 2021 02:21:57: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Thu, 09 Dec 2021 02:21:57: start model_add_line... INFO @ Thu, 09 Dec 2021 02:21:57: start X-correlation... INFO @ Thu, 09 Dec 2021 02:21:57: end of X-cor INFO @ Thu, 09 Dec 2021 02:21:57: #2 finished! INFO @ Thu, 09 Dec 2021 02:21:57: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 02:21:57: #2 alternative fragment length(s) may be 1,45,531 bps INFO @ Thu, 09 Dec 2021 02:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.10_model.r WARNING @ Thu, 09 Dec 2021 02:21:57: #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, 09 Dec 2021 02:21:57: #2 You may need to consider one of the other alternative d(s): 1,45,531 WARNING @ Thu, 09 Dec 2021 02:21:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:21:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:21:58: 15000000 INFO @ Thu, 09 Dec 2021 02:22:05: 16000000 INFO @ Thu, 09 Dec 2021 02:22:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:22:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:22:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.05_summits.bed INFO @ Thu, 09 Dec 2021 02:22:08: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:22:11: 17000000 INFO @ Thu, 09 Dec 2021 02:22:17: 18000000 INFO @ Thu, 09 Dec 2021 02:22:24: 19000000 INFO @ Thu, 09 Dec 2021 02:22:31: 20000000 INFO @ Thu, 09 Dec 2021 02:22:35: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:22:35: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:22:35: #1 total tags in treatment: 20489724 INFO @ Thu, 09 Dec 2021 02:22:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:22:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:22:36: #1 tags after filtering in treatment: 20489724 INFO @ Thu, 09 Dec 2021 02:22:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:22:36: #1 finished! INFO @ Thu, 09 Dec 2021 02:22:36: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:22:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:22:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:22:37: #2 number of paired peaks: 258 WARNING @ Thu, 09 Dec 2021 02:22:37: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Thu, 09 Dec 2021 02:22:37: start model_add_line... INFO @ Thu, 09 Dec 2021 02:22:37: start X-correlation... INFO @ Thu, 09 Dec 2021 02:22:37: end of X-cor INFO @ Thu, 09 Dec 2021 02:22:37: #2 finished! INFO @ Thu, 09 Dec 2021 02:22:37: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 02:22:37: #2 alternative fragment length(s) may be 1,45,531 bps INFO @ Thu, 09 Dec 2021 02:22:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.20_model.r WARNING @ Thu, 09 Dec 2021 02:22:37: #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, 09 Dec 2021 02:22:37: #2 You may need to consider one of the other alternative d(s): 1,45,531 WARNING @ Thu, 09 Dec 2021 02:22:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:22:37: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:22:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:22:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.10_summits.bed INFO @ Thu, 09 Dec 2021 02:22:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:23:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8582554/SRX8582554.20_summits.bed INFO @ Thu, 09 Dec 2021 02:23:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling