Job ID = 14157873 SRX = SRX6799191 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 38761251 spots for SRR10065398/SRR10065398.sra Written 38761251 spots for SRR10065398/SRR10065398.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158057 ("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: 00:09:04 38761251 reads; of these: 38761251 (100.00%) were unpaired; of these: 743842 (1.92%) aligned 0 times 27373172 (70.62%) aligned exactly 1 time 10644237 (27.46%) aligned >1 times 98.08% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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 16 files... [bam_rmdupse_core] 12071086 / 38017409 = 0.3175 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 @ Wed, 08 Dec 2021 12:12:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.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 @ Wed, 08 Dec 2021 12:12:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:12:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:12:22: 1000000 INFO @ Wed, 08 Dec 2021 12:12:27: 2000000 INFO @ Wed, 08 Dec 2021 12:12:33: 3000000 INFO @ Wed, 08 Dec 2021 12:12:38: 4000000 INFO @ Wed, 08 Dec 2021 12:12:43: 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 @ Wed, 08 Dec 2021 12:12:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.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 @ Wed, 08 Dec 2021 12:12:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:12:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:12:49: 6000000 INFO @ Wed, 08 Dec 2021 12:12:54: 1000000 INFO @ Wed, 08 Dec 2021 12:12:56: 7000000 INFO @ Wed, 08 Dec 2021 12:13:01: 2000000 INFO @ Wed, 08 Dec 2021 12:13:03: 8000000 INFO @ Wed, 08 Dec 2021 12:13:09: 3000000 INFO @ Wed, 08 Dec 2021 12:13:10: 9000000 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 @ Wed, 08 Dec 2021 12:13:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.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 @ Wed, 08 Dec 2021 12:13:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:13:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:13:17: 4000000 INFO @ Wed, 08 Dec 2021 12:13:17: 10000000 INFO @ Wed, 08 Dec 2021 12:13:23: 1000000 INFO @ Wed, 08 Dec 2021 12:13:24: 5000000 INFO @ Wed, 08 Dec 2021 12:13:24: 11000000 INFO @ Wed, 08 Dec 2021 12:13:30: 2000000 INFO @ Wed, 08 Dec 2021 12:13:32: 6000000 INFO @ Wed, 08 Dec 2021 12:13:32: 12000000 INFO @ Wed, 08 Dec 2021 12:13:37: 3000000 INFO @ Wed, 08 Dec 2021 12:13:39: 7000000 INFO @ Wed, 08 Dec 2021 12:13:39: 13000000 INFO @ Wed, 08 Dec 2021 12:13:44: 4000000 INFO @ Wed, 08 Dec 2021 12:13:46: 14000000 INFO @ Wed, 08 Dec 2021 12:13:47: 8000000 INFO @ Wed, 08 Dec 2021 12:13:51: 5000000 INFO @ Wed, 08 Dec 2021 12:13:53: 15000000 INFO @ Wed, 08 Dec 2021 12:13:54: 9000000 INFO @ Wed, 08 Dec 2021 12:13:58: 6000000 INFO @ Wed, 08 Dec 2021 12:14:00: 16000000 INFO @ Wed, 08 Dec 2021 12:14:01: 10000000 INFO @ Wed, 08 Dec 2021 12:14:05: 7000000 INFO @ Wed, 08 Dec 2021 12:14:07: 17000000 INFO @ Wed, 08 Dec 2021 12:14:08: 11000000 INFO @ Wed, 08 Dec 2021 12:14:12: 8000000 INFO @ Wed, 08 Dec 2021 12:14:14: 18000000 INFO @ Wed, 08 Dec 2021 12:14:15: 12000000 INFO @ Wed, 08 Dec 2021 12:14:19: 9000000 INFO @ Wed, 08 Dec 2021 12:14:21: 19000000 INFO @ Wed, 08 Dec 2021 12:14:22: 13000000 INFO @ Wed, 08 Dec 2021 12:14:26: 10000000 INFO @ Wed, 08 Dec 2021 12:14:28: 20000000 INFO @ Wed, 08 Dec 2021 12:14:30: 14000000 INFO @ Wed, 08 Dec 2021 12:14:34: 11000000 INFO @ Wed, 08 Dec 2021 12:14:35: 21000000 INFO @ Wed, 08 Dec 2021 12:14:37: 15000000 INFO @ Wed, 08 Dec 2021 12:14:41: 12000000 INFO @ Wed, 08 Dec 2021 12:14:42: 22000000 INFO @ Wed, 08 Dec 2021 12:14:45: 16000000 INFO @ Wed, 08 Dec 2021 12:14:48: 23000000 INFO @ Wed, 08 Dec 2021 12:14:49: 13000000 INFO @ Wed, 08 Dec 2021 12:14:53: 17000000 INFO @ Wed, 08 Dec 2021 12:14:55: 24000000 INFO @ Wed, 08 Dec 2021 12:14:56: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:15:00: 18000000 INFO @ Wed, 08 Dec 2021 12:15:02: 25000000 INFO @ Wed, 08 Dec 2021 12:15:03: 15000000 INFO @ Wed, 08 Dec 2021 12:15:08: 19000000 INFO @ Wed, 08 Dec 2021 12:15:09: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:15:09: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:15:09: #1 total tags in treatment: 25946323 INFO @ Wed, 08 Dec 2021 12:15:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:15:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:15:09: #1 tags after filtering in treatment: 25946323 INFO @ Wed, 08 Dec 2021 12:15:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:15:09: #1 finished! INFO @ Wed, 08 Dec 2021 12:15:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:15:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:15:10: 16000000 INFO @ Wed, 08 Dec 2021 12:15:11: #2 number of paired peaks: 255 WARNING @ Wed, 08 Dec 2021 12:15:11: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Wed, 08 Dec 2021 12:15:11: start model_add_line... INFO @ Wed, 08 Dec 2021 12:15:11: start X-correlation... INFO @ Wed, 08 Dec 2021 12:15:11: end of X-cor INFO @ Wed, 08 Dec 2021 12:15:11: #2 finished! INFO @ Wed, 08 Dec 2021 12:15:11: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:15:11: #2 alternative fragment length(s) may be 1,28,528,555,560,568 bps INFO @ Wed, 08 Dec 2021 12:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05_model.r WARNING @ Wed, 08 Dec 2021 12:15:11: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:15:11: #2 You may need to consider one of the other alternative d(s): 1,28,528,555,560,568 WARNING @ Wed, 08 Dec 2021 12:15:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:15:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:15:16: 20000000 INFO @ Wed, 08 Dec 2021 12:15:17: 17000000 INFO @ Wed, 08 Dec 2021 12:15:23: 18000000 INFO @ Wed, 08 Dec 2021 12:15:24: 21000000 INFO @ Wed, 08 Dec 2021 12:15:30: 19000000 INFO @ Wed, 08 Dec 2021 12:15:31: 22000000 INFO @ Wed, 08 Dec 2021 12:15:37: 20000000 INFO @ Wed, 08 Dec 2021 12:15:39: 23000000 INFO @ Wed, 08 Dec 2021 12:15:44: 21000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:15:46: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:15:47: 24000000 INFO @ Wed, 08 Dec 2021 12:15:51: 22000000 INFO @ Wed, 08 Dec 2021 12:15:55: 25000000 INFO @ Wed, 08 Dec 2021 12:15:58: 23000000 INFO @ Wed, 08 Dec 2021 12:16:02: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:16:02: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:16:02: #1 total tags in treatment: 25946323 INFO @ Wed, 08 Dec 2021 12:16:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:16:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:16:03: #1 tags after filtering in treatment: 25946323 INFO @ Wed, 08 Dec 2021 12:16:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:16:03: #1 finished! INFO @ Wed, 08 Dec 2021 12:16:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05_summits.bed INFO @ Wed, 08 Dec 2021 12:16:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:16:04: #2 number of paired peaks: 255 WARNING @ Wed, 08 Dec 2021 12:16:04: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Wed, 08 Dec 2021 12:16:04: start model_add_line... INFO @ Wed, 08 Dec 2021 12:16:04: 24000000 INFO @ Wed, 08 Dec 2021 12:16:04: start X-correlation... INFO @ Wed, 08 Dec 2021 12:16:04: end of X-cor INFO @ Wed, 08 Dec 2021 12:16:04: #2 finished! INFO @ Wed, 08 Dec 2021 12:16:04: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:16:04: #2 alternative fragment length(s) may be 1,28,528,555,560,568 bps INFO @ Wed, 08 Dec 2021 12:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10_model.r WARNING @ Wed, 08 Dec 2021 12:16:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:16:04: #2 You may need to consider one of the other alternative d(s): 1,28,528,555,560,568 WARNING @ Wed, 08 Dec 2021 12:16:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:16:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:16:10: 25000000 INFO @ Wed, 08 Dec 2021 12:16:16: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:16:16: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:16:16: #1 total tags in treatment: 25946323 INFO @ Wed, 08 Dec 2021 12:16:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:16:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:16:17: #1 tags after filtering in treatment: 25946323 INFO @ Wed, 08 Dec 2021 12:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:16:17: #1 finished! INFO @ Wed, 08 Dec 2021 12:16:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:16:18: #2 number of paired peaks: 255 WARNING @ Wed, 08 Dec 2021 12:16:18: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Wed, 08 Dec 2021 12:16:18: start model_add_line... INFO @ Wed, 08 Dec 2021 12:16:19: start X-correlation... INFO @ Wed, 08 Dec 2021 12:16:19: end of X-cor INFO @ Wed, 08 Dec 2021 12:16:19: #2 finished! INFO @ Wed, 08 Dec 2021 12:16:19: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 12:16:19: #2 alternative fragment length(s) may be 1,28,528,555,560,568 bps INFO @ Wed, 08 Dec 2021 12:16:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20_model.r WARNING @ Wed, 08 Dec 2021 12:16:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:16:19: #2 You may need to consider one of the other alternative d(s): 1,28,528,555,560,568 WARNING @ Wed, 08 Dec 2021 12:16:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:16:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:16:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:16:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:16:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10_summits.bed INFO @ Wed, 08 Dec 2021 12:16:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20_summits.bed INFO @ Wed, 08 Dec 2021 12:17:09: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling