Job ID = 10165778 SRX = SRX9120613 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 37768674 spots for SRR12638556/SRR12638556.sra Written 37768674 spots for SRR12638556/SRR12638556.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166095 ("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: 00:06:32 37768674 reads; of these: 37768674 (100.00%) were unpaired; of these: 12273659 (32.50%) aligned 0 times 21159216 (56.02%) aligned exactly 1 time 4335799 (11.48%) aligned >1 times 67.50% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:33 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] 4316371 / 25495015 = 0.1693 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 20:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.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 20:05:24: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:24: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:29: 1000000 INFO @ Thu, 08 Oct 2020 20:05:34: 2000000 INFO @ Thu, 08 Oct 2020 20:05:39: 3000000 INFO @ Thu, 08 Oct 2020 20:05:44: 4000000 INFO @ Thu, 08 Oct 2020 20:05:50: 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 20:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.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 20:05:53: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:53: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:55: 6000000 INFO @ Thu, 08 Oct 2020 20:05:58: 1000000 INFO @ Thu, 08 Oct 2020 20:06:00: 7000000 INFO @ Thu, 08 Oct 2020 20:06:03: 2000000 INFO @ Thu, 08 Oct 2020 20:06:05: 8000000 INFO @ Thu, 08 Oct 2020 20:06:09: 3000000 INFO @ Thu, 08 Oct 2020 20:06:10: 9000000 INFO @ Thu, 08 Oct 2020 20:06:14: 4000000 INFO @ Thu, 08 Oct 2020 20:06:15: 10000000 INFO @ Thu, 08 Oct 2020 20:06:19: 5000000 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 20:06:20: 11000000 INFO @ Thu, 08 Oct 2020 20:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.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 20:06:23: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:06:23: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:06:25: 6000000 INFO @ Thu, 08 Oct 2020 20:06:26: 12000000 INFO @ Thu, 08 Oct 2020 20:06:28: 1000000 INFO @ Thu, 08 Oct 2020 20:06:30: 7000000 INFO @ Thu, 08 Oct 2020 20:06:31: 13000000 INFO @ Thu, 08 Oct 2020 20:06:33: 2000000 INFO @ Thu, 08 Oct 2020 20:06:36: 8000000 INFO @ Thu, 08 Oct 2020 20:06:37: 14000000 INFO @ Thu, 08 Oct 2020 20:06:39: 3000000 INFO @ Thu, 08 Oct 2020 20:06:41: 9000000 INFO @ Thu, 08 Oct 2020 20:06:42: 15000000 INFO @ Thu, 08 Oct 2020 20:06:44: 4000000 INFO @ Thu, 08 Oct 2020 20:06:46: 10000000 INFO @ Thu, 08 Oct 2020 20:06:47: 16000000 INFO @ Thu, 08 Oct 2020 20:06:50: 5000000 INFO @ Thu, 08 Oct 2020 20:06:53: 11000000 INFO @ Thu, 08 Oct 2020 20:06:53: 17000000 INFO @ Thu, 08 Oct 2020 20:06:55: 6000000 INFO @ Thu, 08 Oct 2020 20:06:58: 12000000 INFO @ Thu, 08 Oct 2020 20:06:58: 18000000 INFO @ Thu, 08 Oct 2020 20:07:00: 7000000 INFO @ Thu, 08 Oct 2020 20:07:03: 13000000 INFO @ Thu, 08 Oct 2020 20:07:04: 19000000 INFO @ Thu, 08 Oct 2020 20:07:06: 8000000 INFO @ Thu, 08 Oct 2020 20:07:09: 14000000 INFO @ Thu, 08 Oct 2020 20:07:09: 20000000 INFO @ Thu, 08 Oct 2020 20:07:11: 9000000 INFO @ Thu, 08 Oct 2020 20:07:14: 15000000 INFO @ Thu, 08 Oct 2020 20:07:15: 21000000 INFO @ Thu, 08 Oct 2020 20:07:16: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:16: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:16: #1 total tags in treatment: 21178644 INFO @ Thu, 08 Oct 2020 20:07:16: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:16: #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 20:07:16: #1 tags after filtering in treatment: 21178644 INFO @ Thu, 08 Oct 2020 20:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:16: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:16: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:16: 10000000 INFO @ Thu, 08 Oct 2020 20:07:17: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 20:07:17: 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 20:07:17: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:18: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:18: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:18: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:18: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:07:18: #2 alternative fragment length(s) may be 1,26,593 bps INFO @ Thu, 08 Oct 2020 20:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.05_model.r WARNING @ Thu, 08 Oct 2020 20:07:18: #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 20:07:18: #2 You may need to consider one of the other alternative d(s): 1,26,593 WARNING @ Thu, 08 Oct 2020 20:07:18: #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 20:07:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:20: 16000000 INFO @ Thu, 08 Oct 2020 20:07:22: 11000000 INFO @ Thu, 08 Oct 2020 20:07:25: 17000000 INFO @ Thu, 08 Oct 2020 20:07:27: 12000000 INFO @ Thu, 08 Oct 2020 20:07:30: 18000000 INFO @ Thu, 08 Oct 2020 20:07:32: 13000000 INFO @ Thu, 08 Oct 2020 20:07:35: 19000000 INFO @ Thu, 08 Oct 2020 20:07:37: 14000000 INFO @ Thu, 08 Oct 2020 20:07:40: 20000000 INFO @ Thu, 08 Oct 2020 20:07:42: 15000000 INFO @ Thu, 08 Oct 2020 20:07:45: 21000000 INFO @ Thu, 08 Oct 2020 20:07:46: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:46: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:46: #1 total tags in treatment: 21178644 INFO @ Thu, 08 Oct 2020 20:07:46: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:46: #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 20:07:47: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:47: #1 tags after filtering in treatment: 21178644 INFO @ Thu, 08 Oct 2020 20:07:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:47: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:47: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:47: 16000000 INFO @ Thu, 08 Oct 2020 20:07:48: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 20:07:48: 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 20:07:48: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:48: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:48: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:48: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:48: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:07:48: #2 alternative fragment length(s) may be 1,26,593 bps INFO @ Thu, 08 Oct 2020 20:07:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.10_model.r WARNING @ Thu, 08 Oct 2020 20:07:48: #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 20:07:48: #2 You may need to consider one of the other alternative d(s): 1,26,593 WARNING @ Thu, 08 Oct 2020 20:07:48: #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 20:07:48: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:52: 17000000 INFO @ Thu, 08 Oct 2020 20:07:57: 18000000 INFO @ Thu, 08 Oct 2020 20:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:08:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.05_summits.bed INFO @ Thu, 08 Oct 2020 20:08:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:08:02: 19000000 INFO @ Thu, 08 Oct 2020 20:08:07: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:08:12: 21000000 INFO @ Thu, 08 Oct 2020 20:08:13: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:08:13: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:08:13: #1 total tags in treatment: 21178644 INFO @ Thu, 08 Oct 2020 20:08:13: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:08:13: #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 20:08:14: #1 tags after filtering in treatment: 21178644 INFO @ Thu, 08 Oct 2020 20:08:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:08:14: #1 finished! INFO @ Thu, 08 Oct 2020 20:08:14: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:08:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:08:15: #2 number of paired peaks: 199 WARNING @ Thu, 08 Oct 2020 20:08:15: 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 20:08:15: start model_add_line... INFO @ Thu, 08 Oct 2020 20:08:15: start X-correlation... INFO @ Thu, 08 Oct 2020 20:08:15: end of X-cor INFO @ Thu, 08 Oct 2020 20:08:15: #2 finished! INFO @ Thu, 08 Oct 2020 20:08:15: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:08:15: #2 alternative fragment length(s) may be 1,26,593 bps INFO @ Thu, 08 Oct 2020 20:08:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.20_model.r WARNING @ Thu, 08 Oct 2020 20:08:15: #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 20:08:15: #2 You may need to consider one of the other alternative d(s): 1,26,593 WARNING @ Thu, 08 Oct 2020 20:08:15: #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 20:08:15: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:08:17: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:08:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:08:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.10_summits.bed INFO @ Thu, 08 Oct 2020 20:08:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:08:44: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120613/SRX9120613.20_summits.bed INFO @ Thu, 08 Oct 2020 20:08:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。