Job ID = 10165784 SRX = SRX9120617 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27905994 spots for SRR12638560/SRR12638560.sra Written 27905994 spots for SRR12638560/SRR12638560.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166112 ("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 27905994 reads; of these: 27905994 (100.00%) were unpaired; of these: 1405044 (5.03%) aligned 0 times 22146991 (79.36%) aligned exactly 1 time 4353959 (15.60%) aligned >1 times 94.97% 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] 4354166 / 26500950 = 0.1643 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 20:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.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 20:04:52: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:52: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:57: 1000000 INFO @ Thu, 08 Oct 2020 20:05:02: 2000000 INFO @ Thu, 08 Oct 2020 20:05:06: 3000000 INFO @ Thu, 08 Oct 2020 20:05:11: 4000000 INFO @ Thu, 08 Oct 2020 20:05:16: 5000000 INFO @ Thu, 08 Oct 2020 20:05:20: 6000000 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 20:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.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 20:05:22: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:22: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:25: 7000000 INFO @ Thu, 08 Oct 2020 20:05:28: 1000000 INFO @ Thu, 08 Oct 2020 20:05:30: 8000000 INFO @ Thu, 08 Oct 2020 20:05:33: 2000000 INFO @ Thu, 08 Oct 2020 20:05:35: 9000000 INFO @ Thu, 08 Oct 2020 20:05:38: 3000000 INFO @ Thu, 08 Oct 2020 20:05:40: 10000000 INFO @ Thu, 08 Oct 2020 20:05:44: 4000000 INFO @ Thu, 08 Oct 2020 20:05:45: 11000000 INFO @ Thu, 08 Oct 2020 20:05:49: 5000000 INFO @ Thu, 08 Oct 2020 20:05:50: 12000000 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 20:05:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.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 20:05:52: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:52: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:54: 6000000 INFO @ Thu, 08 Oct 2020 20:05:55: 13000000 INFO @ Thu, 08 Oct 2020 20:05:57: 1000000 INFO @ Thu, 08 Oct 2020 20:05:59: 7000000 INFO @ Thu, 08 Oct 2020 20:05:59: 14000000 INFO @ Thu, 08 Oct 2020 20:06:02: 2000000 INFO @ Thu, 08 Oct 2020 20:06:04: 15000000 INFO @ Thu, 08 Oct 2020 20:06:05: 8000000 INFO @ Thu, 08 Oct 2020 20:06:08: 3000000 INFO @ Thu, 08 Oct 2020 20:06:09: 16000000 INFO @ Thu, 08 Oct 2020 20:06:10: 9000000 INFO @ Thu, 08 Oct 2020 20:06:13: 4000000 INFO @ Thu, 08 Oct 2020 20:06:14: 17000000 INFO @ Thu, 08 Oct 2020 20:06:15: 10000000 INFO @ Thu, 08 Oct 2020 20:06:18: 5000000 INFO @ Thu, 08 Oct 2020 20:06:19: 18000000 INFO @ Thu, 08 Oct 2020 20:06:20: 11000000 INFO @ Thu, 08 Oct 2020 20:06:23: 6000000 INFO @ Thu, 08 Oct 2020 20:06:24: 19000000 INFO @ Thu, 08 Oct 2020 20:06:26: 12000000 INFO @ Thu, 08 Oct 2020 20:06:27: 7000000 INFO @ Thu, 08 Oct 2020 20:06:29: 20000000 INFO @ Thu, 08 Oct 2020 20:06:31: 13000000 INFO @ Thu, 08 Oct 2020 20:06:32: 8000000 INFO @ Thu, 08 Oct 2020 20:06:33: 21000000 INFO @ Thu, 08 Oct 2020 20:06:36: 14000000 INFO @ Thu, 08 Oct 2020 20:06:37: 9000000 INFO @ Thu, 08 Oct 2020 20:06:38: 22000000 INFO @ Thu, 08 Oct 2020 20:06:39: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:39: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:39: #1 total tags in treatment: 22146784 INFO @ Thu, 08 Oct 2020 20:06:39: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:39: #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 20:06:39: #1 tags after filtering in treatment: 22146784 INFO @ Thu, 08 Oct 2020 20:06:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:39: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:39: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:41: #2 number of paired peaks: 171 WARNING @ Thu, 08 Oct 2020 20:06:41: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:41: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:41: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:41: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:41: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:41: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:06:41: #2 alternative fragment length(s) may be 1,11,43,542 bps INFO @ Thu, 08 Oct 2020 20:06:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.05_model.r WARNING @ Thu, 08 Oct 2020 20:06:41: #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 20:06:41: #2 You may need to consider one of the other alternative d(s): 1,11,43,542 WARNING @ Thu, 08 Oct 2020 20:06:41: #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 20:06:41: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:42: 15000000 INFO @ Thu, 08 Oct 2020 20:06:42: 10000000 INFO @ Thu, 08 Oct 2020 20:06:47: 16000000 INFO @ Thu, 08 Oct 2020 20:06:47: 11000000 INFO @ Thu, 08 Oct 2020 20:06:53: 12000000 INFO @ Thu, 08 Oct 2020 20:06:53: 17000000 INFO @ Thu, 08 Oct 2020 20:06:58: 13000000 INFO @ Thu, 08 Oct 2020 20:06:58: 18000000 INFO @ Thu, 08 Oct 2020 20:07:03: 14000000 INFO @ Thu, 08 Oct 2020 20:07:04: 19000000 INFO @ Thu, 08 Oct 2020 20:07:08: 15000000 INFO @ Thu, 08 Oct 2020 20:07:10: 20000000 INFO @ Thu, 08 Oct 2020 20:07:13: 16000000 INFO @ Thu, 08 Oct 2020 20:07:15: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:15: 21000000 INFO @ Thu, 08 Oct 2020 20:07:18: 17000000 INFO @ Thu, 08 Oct 2020 20:07:21: 22000000 INFO @ Thu, 08 Oct 2020 20:07:22: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:22: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:22: #1 total tags in treatment: 22146784 INFO @ Thu, 08 Oct 2020 20:07:22: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:22: #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 20:07:22: #1 tags after filtering in treatment: 22146784 INFO @ Thu, 08 Oct 2020 20:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:22: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:22: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:23: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:07:23: #2 number of paired peaks: 171 WARNING @ Thu, 08 Oct 2020 20:07:23: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Thu, 08 Oct 2020 20:07:23: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:24: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:24: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:24: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:24: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:07:24: #2 alternative fragment length(s) may be 1,11,43,542 bps INFO @ Thu, 08 Oct 2020 20:07:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.10_model.r WARNING @ Thu, 08 Oct 2020 20:07:24: #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 20:07:24: #2 You may need to consider one of the other alternative d(s): 1,11,43,542 WARNING @ Thu, 08 Oct 2020 20:07:24: #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 20:07:24: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:28: 19000000 INFO @ Thu, 08 Oct 2020 20:07:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.05_summits.bed INFO @ Thu, 08 Oct 2020 20:07:31: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:07:32: 20000000 INFO @ Thu, 08 Oct 2020 20:07:37: 21000000 INFO @ Thu, 08 Oct 2020 20:07:42: 22000000 INFO @ Thu, 08 Oct 2020 20:07:43: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:43: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:43: #1 total tags in treatment: 22146784 INFO @ Thu, 08 Oct 2020 20:07:43: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:43: #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 20:07:43: #1 tags after filtering in treatment: 22146784 INFO @ Thu, 08 Oct 2020 20:07:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:43: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:43: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:44: #2 number of paired peaks: 171 WARNING @ Thu, 08 Oct 2020 20:07:44: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Thu, 08 Oct 2020 20:07:44: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:44: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:44: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:44: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:44: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:07:44: #2 alternative fragment length(s) may be 1,11,43,542 bps INFO @ Thu, 08 Oct 2020 20:07:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.20_model.r WARNING @ Thu, 08 Oct 2020 20:07:44: #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 20:07:44: #2 You may need to consider one of the other alternative d(s): 1,11,43,542 WARNING @ Thu, 08 Oct 2020 20:07:44: #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 20:07:44: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.10_summits.bed INFO @ Thu, 08 Oct 2020 20:08:15: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:08:18: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:08:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:08:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:08:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120617/SRX9120617.20_summits.bed INFO @ Thu, 08 Oct 2020 20:08:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling