Job ID = 14160536 SRX = SRX7505499 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 47572384 spots for SRR10832157/SRR10832157.sra Written 47572384 spots for SRR10832157/SRR10832157.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160688 ("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: 00:09:23 47572384 reads; of these: 47572384 (100.00%) were unpaired; of these: 2606284 (5.48%) aligned 0 times 36766932 (77.29%) aligned exactly 1 time 8199168 (17.24%) aligned >1 times 94.52% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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 20 files... [bam_rmdupse_core] 18227240 / 44966100 = 0.4054 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 03:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.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 03:22:44: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:22:44: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:22:49: 1000000 INFO @ Thu, 09 Dec 2021 03:22:54: 2000000 INFO @ Thu, 09 Dec 2021 03:22:59: 3000000 INFO @ Thu, 09 Dec 2021 03:23:04: 4000000 INFO @ Thu, 09 Dec 2021 03:23:08: 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 03:23:13: 6000000 INFO @ Thu, 09 Dec 2021 03:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.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 03:23:14: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:23:14: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:23:18: 7000000 INFO @ Thu, 09 Dec 2021 03:23:19: 1000000 INFO @ Thu, 09 Dec 2021 03:23:23: 8000000 INFO @ Thu, 09 Dec 2021 03:23:24: 2000000 INFO @ Thu, 09 Dec 2021 03:23:27: 9000000 INFO @ Thu, 09 Dec 2021 03:23:29: 3000000 INFO @ Thu, 09 Dec 2021 03:23:32: 10000000 INFO @ Thu, 09 Dec 2021 03:23:34: 4000000 INFO @ Thu, 09 Dec 2021 03:23:37: 11000000 INFO @ Thu, 09 Dec 2021 03:23:39: 5000000 INFO @ Thu, 09 Dec 2021 03:23:42: 12000000 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 03:23:44: 6000000 INFO @ Thu, 09 Dec 2021 03:23:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.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 03:23:44: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:23:44: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:23:47: 13000000 INFO @ Thu, 09 Dec 2021 03:23:49: 7000000 INFO @ Thu, 09 Dec 2021 03:23:50: 1000000 INFO @ Thu, 09 Dec 2021 03:23:52: 14000000 INFO @ Thu, 09 Dec 2021 03:23:54: 8000000 INFO @ Thu, 09 Dec 2021 03:23:55: 2000000 INFO @ Thu, 09 Dec 2021 03:23:57: 15000000 INFO @ Thu, 09 Dec 2021 03:23:59: 9000000 INFO @ Thu, 09 Dec 2021 03:24:01: 3000000 INFO @ Thu, 09 Dec 2021 03:24:02: 16000000 INFO @ Thu, 09 Dec 2021 03:24:04: 10000000 INFO @ Thu, 09 Dec 2021 03:24:07: 4000000 INFO @ Thu, 09 Dec 2021 03:24:07: 17000000 INFO @ Thu, 09 Dec 2021 03:24:09: 11000000 INFO @ Thu, 09 Dec 2021 03:24:12: 5000000 INFO @ Thu, 09 Dec 2021 03:24:12: 18000000 INFO @ Thu, 09 Dec 2021 03:24:14: 12000000 INFO @ Thu, 09 Dec 2021 03:24:18: 19000000 INFO @ Thu, 09 Dec 2021 03:24:18: 6000000 INFO @ Thu, 09 Dec 2021 03:24:19: 13000000 INFO @ Thu, 09 Dec 2021 03:24:23: 20000000 INFO @ Thu, 09 Dec 2021 03:24:23: 7000000 INFO @ Thu, 09 Dec 2021 03:24:24: 14000000 INFO @ Thu, 09 Dec 2021 03:24:28: 21000000 INFO @ Thu, 09 Dec 2021 03:24:29: 8000000 INFO @ Thu, 09 Dec 2021 03:24:30: 15000000 INFO @ Thu, 09 Dec 2021 03:24:33: 22000000 INFO @ Thu, 09 Dec 2021 03:24:35: 16000000 INFO @ Thu, 09 Dec 2021 03:24:35: 9000000 INFO @ Thu, 09 Dec 2021 03:24:38: 23000000 INFO @ Thu, 09 Dec 2021 03:24:40: 17000000 INFO @ Thu, 09 Dec 2021 03:24:40: 10000000 INFO @ Thu, 09 Dec 2021 03:24:43: 24000000 INFO @ Thu, 09 Dec 2021 03:24:45: 18000000 INFO @ Thu, 09 Dec 2021 03:24:46: 11000000 INFO @ Thu, 09 Dec 2021 03:24:48: 25000000 INFO @ Thu, 09 Dec 2021 03:24:50: 19000000 INFO @ Thu, 09 Dec 2021 03:24:52: 12000000 INFO @ Thu, 09 Dec 2021 03:24:53: 26000000 INFO @ Thu, 09 Dec 2021 03:24:55: 20000000 INFO @ Thu, 09 Dec 2021 03:24:57: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:24:57: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:24:57: #1 total tags in treatment: 26738860 INFO @ Thu, 09 Dec 2021 03:24:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:24:57: #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 03:24:57: 13000000 INFO @ Thu, 09 Dec 2021 03:24:57: #1 tags after filtering in treatment: 26738860 INFO @ Thu, 09 Dec 2021 03:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:24:57: #1 finished! INFO @ Thu, 09 Dec 2021 03:24:57: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:24:59: #2 number of paired peaks: 119 WARNING @ Thu, 09 Dec 2021 03:24:59: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Thu, 09 Dec 2021 03:24:59: start model_add_line... INFO @ Thu, 09 Dec 2021 03:24:59: start X-correlation... INFO @ Thu, 09 Dec 2021 03:24:59: end of X-cor INFO @ Thu, 09 Dec 2021 03:24:59: #2 finished! INFO @ Thu, 09 Dec 2021 03:24:59: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 03:24:59: #2 alternative fragment length(s) may be 1,29,46,115,121,169,543,574 bps INFO @ Thu, 09 Dec 2021 03:24:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05_model.r WARNING @ Thu, 09 Dec 2021 03:24:59: #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 03:24:59: #2 You may need to consider one of the other alternative d(s): 1,29,46,115,121,169,543,574 WARNING @ Thu, 09 Dec 2021 03:24:59: #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 03:24:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:24:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:25:00: 21000000 INFO @ Thu, 09 Dec 2021 03:25:03: 14000000 INFO @ Thu, 09 Dec 2021 03:25:05: 22000000 INFO @ Thu, 09 Dec 2021 03:25:09: 15000000 INFO @ Thu, 09 Dec 2021 03:25:10: 23000000 INFO @ Thu, 09 Dec 2021 03:25:14: 16000000 INFO @ Thu, 09 Dec 2021 03:25:15: 24000000 INFO @ Thu, 09 Dec 2021 03:25:20: 17000000 INFO @ Thu, 09 Dec 2021 03:25:20: 25000000 INFO @ Thu, 09 Dec 2021 03:25:25: 26000000 INFO @ Thu, 09 Dec 2021 03:25:26: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:25:29: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:25:29: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:25:29: #1 total tags in treatment: 26738860 INFO @ Thu, 09 Dec 2021 03:25:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:25:29: #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 03:25:29: #1 tags after filtering in treatment: 26738860 INFO @ Thu, 09 Dec 2021 03:25:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:25:29: #1 finished! INFO @ Thu, 09 Dec 2021 03:25:29: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:25:31: #2 number of paired peaks: 119 WARNING @ Thu, 09 Dec 2021 03:25:31: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Thu, 09 Dec 2021 03:25:31: start model_add_line... INFO @ Thu, 09 Dec 2021 03:25:31: start X-correlation... INFO @ Thu, 09 Dec 2021 03:25:31: end of X-cor INFO @ Thu, 09 Dec 2021 03:25:31: #2 finished! INFO @ Thu, 09 Dec 2021 03:25:31: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 03:25:31: #2 alternative fragment length(s) may be 1,29,46,115,121,169,543,574 bps INFO @ Thu, 09 Dec 2021 03:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10_model.r WARNING @ Thu, 09 Dec 2021 03:25:31: #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 03:25:31: #2 You may need to consider one of the other alternative d(s): 1,29,46,115,121,169,543,574 WARNING @ Thu, 09 Dec 2021 03:25:31: #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 03:25:31: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:25:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:25:31: 19000000 INFO @ Thu, 09 Dec 2021 03:25:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:25:37: 20000000 INFO @ Thu, 09 Dec 2021 03:25:42: 21000000 INFO @ Thu, 09 Dec 2021 03:25:48: 22000000 INFO @ Thu, 09 Dec 2021 03:25:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:25:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:25:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05_summits.bed INFO @ Thu, 09 Dec 2021 03:25:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:25:53: 23000000 INFO @ Thu, 09 Dec 2021 03:25:58: 24000000 INFO @ Thu, 09 Dec 2021 03:26:04: 25000000 INFO @ Thu, 09 Dec 2021 03:26:07: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:26:09: 26000000 INFO @ Thu, 09 Dec 2021 03:26:13: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:26:13: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:26:13: #1 total tags in treatment: 26738860 INFO @ Thu, 09 Dec 2021 03:26:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:26:13: #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 03:26:14: #1 tags after filtering in treatment: 26738860 INFO @ Thu, 09 Dec 2021 03:26:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:26:14: #1 finished! INFO @ Thu, 09 Dec 2021 03:26:14: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:26:15: #2 number of paired peaks: 119 WARNING @ Thu, 09 Dec 2021 03:26:15: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Thu, 09 Dec 2021 03:26:15: start model_add_line... INFO @ Thu, 09 Dec 2021 03:26:16: start X-correlation... INFO @ Thu, 09 Dec 2021 03:26:16: end of X-cor INFO @ Thu, 09 Dec 2021 03:26:16: #2 finished! INFO @ Thu, 09 Dec 2021 03:26:16: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 03:26:16: #2 alternative fragment length(s) may be 1,29,46,115,121,169,543,574 bps INFO @ Thu, 09 Dec 2021 03:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20_model.r WARNING @ Thu, 09 Dec 2021 03:26:16: #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 03:26:16: #2 You may need to consider one of the other alternative d(s): 1,29,46,115,121,169,543,574 WARNING @ Thu, 09 Dec 2021 03:26:16: #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 03:26:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:26:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10_summits.bed INFO @ Thu, 09 Dec 2021 03:26:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:26:51: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:27:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:27:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:27:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20_summits.bed INFO @ Thu, 09 Dec 2021 03:27:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling