Job ID = 16432259 SRX = SRX15407774 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:31:55 prefetch.2.10.7: 1) Downloading 'SRR19348976'... 2022-08-02T00:31:55 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:33:07 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:33:07 prefetch.2.10.7: 1) 'SRR19348976' was downloaded successfully 2022-08-02T00:33:07 prefetch.2.10.7: 'SRR19348976' has 0 unresolved dependencies Read 31369868 spots for SRR19348976/SRR19348976.sra Written 31369868 spots for SRR19348976/SRR19348976.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434141 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:54 31369868 reads; of these: 31369868 (100.00%) were unpaired; of these: 1646784 (5.25%) aligned 0 times 26141568 (83.33%) aligned exactly 1 time 3581516 (11.42%) aligned >1 times 94.75% overall alignment rate Time searching: 00:08:55 Overall time: 00:08:55 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] 7936702 / 29723084 = 0.2670 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:50:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.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 @ Tue, 02 Aug 2022 09:50:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:50:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:32: 1000000 INFO @ Tue, 02 Aug 2022 09:50:39: 2000000 INFO @ Tue, 02 Aug 2022 09:50:45: 3000000 INFO @ Tue, 02 Aug 2022 09:50:52: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:50:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.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 @ Tue, 02 Aug 2022 09:50:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:50:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:50:59: 5000000 INFO @ Tue, 02 Aug 2022 09:51:03: 1000000 INFO @ Tue, 02 Aug 2022 09:51:07: 6000000 INFO @ Tue, 02 Aug 2022 09:51:11: 2000000 INFO @ Tue, 02 Aug 2022 09:51:14: 7000000 INFO @ Tue, 02 Aug 2022 09:51:19: 3000000 INFO @ Tue, 02 Aug 2022 09:51:21: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:51:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.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 @ Tue, 02 Aug 2022 09:51:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:51:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:51:27: 4000000 INFO @ Tue, 02 Aug 2022 09:51:28: 9000000 INFO @ Tue, 02 Aug 2022 09:51:33: 1000000 INFO @ Tue, 02 Aug 2022 09:51:35: 5000000 INFO @ Tue, 02 Aug 2022 09:51:36: 10000000 INFO @ Tue, 02 Aug 2022 09:51:41: 2000000 INFO @ Tue, 02 Aug 2022 09:51:42: 6000000 INFO @ Tue, 02 Aug 2022 09:51:43: 11000000 INFO @ Tue, 02 Aug 2022 09:51:49: 3000000 INFO @ Tue, 02 Aug 2022 09:51:50: 7000000 INFO @ Tue, 02 Aug 2022 09:51:51: 12000000 INFO @ Tue, 02 Aug 2022 09:51:57: 4000000 INFO @ Tue, 02 Aug 2022 09:51:57: 8000000 INFO @ Tue, 02 Aug 2022 09:51:58: 13000000 INFO @ Tue, 02 Aug 2022 09:52:04: 5000000 INFO @ Tue, 02 Aug 2022 09:52:05: 9000000 INFO @ Tue, 02 Aug 2022 09:52:06: 14000000 INFO @ Tue, 02 Aug 2022 09:52:12: 6000000 INFO @ Tue, 02 Aug 2022 09:52:12: 10000000 INFO @ Tue, 02 Aug 2022 09:52:13: 15000000 INFO @ Tue, 02 Aug 2022 09:52:19: 7000000 INFO @ Tue, 02 Aug 2022 09:52:20: 11000000 INFO @ Tue, 02 Aug 2022 09:52:20: 16000000 INFO @ Tue, 02 Aug 2022 09:52:27: 8000000 INFO @ Tue, 02 Aug 2022 09:52:27: 12000000 INFO @ Tue, 02 Aug 2022 09:52:28: 17000000 INFO @ Tue, 02 Aug 2022 09:52:34: 9000000 INFO @ Tue, 02 Aug 2022 09:52:35: 13000000 INFO @ Tue, 02 Aug 2022 09:52:35: 18000000 INFO @ Tue, 02 Aug 2022 09:52:41: 10000000 INFO @ Tue, 02 Aug 2022 09:52:42: 14000000 INFO @ Tue, 02 Aug 2022 09:52:42: 19000000 INFO @ Tue, 02 Aug 2022 09:52:49: 11000000 INFO @ Tue, 02 Aug 2022 09:52:49: 15000000 INFO @ Tue, 02 Aug 2022 09:52:50: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:52:57: 12000000 INFO @ Tue, 02 Aug 2022 09:52:57: 21000000 INFO @ Tue, 02 Aug 2022 09:52:57: 16000000 INFO @ Tue, 02 Aug 2022 09:53:03: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:53:03: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:53:03: #1 total tags in treatment: 21786382 INFO @ Tue, 02 Aug 2022 09:53:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:53:04: #1 tags after filtering in treatment: 21786382 INFO @ Tue, 02 Aug 2022 09:53:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:04: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:04: 13000000 INFO @ Tue, 02 Aug 2022 09:53:05: #2 number of paired peaks: 604 WARNING @ Tue, 02 Aug 2022 09:53:05: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Tue, 02 Aug 2022 09:53:05: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:05: 17000000 INFO @ Tue, 02 Aug 2022 09:53:05: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:05: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:05: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:05: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 09:53:05: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 09:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.05_model.r INFO @ Tue, 02 Aug 2022 09:53:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:53:12: 14000000 INFO @ Tue, 02 Aug 2022 09:53:13: 18000000 INFO @ Tue, 02 Aug 2022 09:53:20: 15000000 INFO @ Tue, 02 Aug 2022 09:53:20: 19000000 INFO @ Tue, 02 Aug 2022 09:53:27: 16000000 INFO @ Tue, 02 Aug 2022 09:53:27: 20000000 INFO @ Tue, 02 Aug 2022 09:53:34: 17000000 INFO @ Tue, 02 Aug 2022 09:53:35: 21000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:53:40: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:53:40: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:53:40: #1 total tags in treatment: 21786382 INFO @ Tue, 02 Aug 2022 09:53:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:53:41: #1 tags after filtering in treatment: 21786382 INFO @ Tue, 02 Aug 2022 09:53:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:41: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:42: 18000000 INFO @ Tue, 02 Aug 2022 09:53:42: #2 number of paired peaks: 604 WARNING @ Tue, 02 Aug 2022 09:53:42: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Tue, 02 Aug 2022 09:53:42: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:42: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:42: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:42: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:42: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 09:53:42: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 09:53:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.10_model.r INFO @ Tue, 02 Aug 2022 09:53:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:53:49: 19000000 INFO @ Tue, 02 Aug 2022 09:53:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:53:56: 20000000 INFO @ Tue, 02 Aug 2022 09:54:02: 21000000 INFO @ Tue, 02 Aug 2022 09:54:07: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:54:07: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:54:07: #1 total tags in treatment: 21786382 INFO @ Tue, 02 Aug 2022 09:54:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:54:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:54:07: #1 tags after filtering in treatment: 21786382 INFO @ Tue, 02 Aug 2022 09:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:54:07: #1 finished! INFO @ Tue, 02 Aug 2022 09:54:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:54:09: #2 number of paired peaks: 604 WARNING @ Tue, 02 Aug 2022 09:54:09: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Tue, 02 Aug 2022 09:54:09: start model_add_line... INFO @ Tue, 02 Aug 2022 09:54:09: start X-correlation... INFO @ Tue, 02 Aug 2022 09:54:09: end of X-cor INFO @ Tue, 02 Aug 2022 09:54:09: #2 finished! INFO @ Tue, 02 Aug 2022 09:54:09: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 09:54:09: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 09:54:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.20_model.r INFO @ Tue, 02 Aug 2022 09:54:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.05_summits.bed INFO @ Tue, 02 Aug 2022 09:54:13: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14235 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:54:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:54:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.10_summits.bed INFO @ Tue, 02 Aug 2022 09:54:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (10975 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:54:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:55:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:55:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:55:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407774/SRX15407774.20_summits.bed INFO @ Tue, 02 Aug 2022 09:55:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7617 records, 4 fields): 30 millis CompletedMACS2peakCalling