Job ID = 6366520 SRX = SRX1674100 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:50:26 prefetch.2.10.7: 1) Downloading 'SRR3320146'... 2020-06-15T22:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:53:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:53:19 prefetch.2.10.7: 1) 'SRR3320146' was downloaded successfully Read 57625311 spots for SRR3320146/SRR3320146.sra Written 57625311 spots for SRR3320146/SRR3320146.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:23 57625311 reads; of these: 57625311 (100.00%) were unpaired; of these: 2027559 (3.52%) aligned 0 times 49469702 (85.85%) aligned exactly 1 time 6128050 (10.63%) aligned >1 times 96.48% overall alignment rate Time searching: 00:12:23 Overall time: 00:12:23 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 24 files... [bam_rmdupse_core] 24645984 / 55597752 = 0.4433 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 @ Tue, 16 Jun 2020 08:19:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.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, 16 Jun 2020 08:19:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:54: 1000000 INFO @ Tue, 16 Jun 2020 08:20:00: 2000000 INFO @ Tue, 16 Jun 2020 08:20:06: 3000000 INFO @ Tue, 16 Jun 2020 08:20:11: 4000000 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 @ Tue, 16 Jun 2020 08:20:17: 5000000 INFO @ Tue, 16 Jun 2020 08:20:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.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, 16 Jun 2020 08:20:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:24: 6000000 INFO @ Tue, 16 Jun 2020 08:20:24: 1000000 INFO @ Tue, 16 Jun 2020 08:20:30: 2000000 INFO @ Tue, 16 Jun 2020 08:20:30: 7000000 INFO @ Tue, 16 Jun 2020 08:20:36: 3000000 INFO @ Tue, 16 Jun 2020 08:20:36: 8000000 INFO @ Tue, 16 Jun 2020 08:20:42: 4000000 INFO @ Tue, 16 Jun 2020 08:20:43: 9000000 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 @ Tue, 16 Jun 2020 08:20:48: 5000000 INFO @ Tue, 16 Jun 2020 08:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.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, 16 Jun 2020 08:20:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:49: 10000000 INFO @ Tue, 16 Jun 2020 08:20:54: 6000000 INFO @ Tue, 16 Jun 2020 08:20:54: 1000000 INFO @ Tue, 16 Jun 2020 08:20:56: 11000000 INFO @ Tue, 16 Jun 2020 08:21:00: 7000000 INFO @ Tue, 16 Jun 2020 08:21:01: 2000000 INFO @ Tue, 16 Jun 2020 08:21:02: 12000000 INFO @ Tue, 16 Jun 2020 08:21:06: 8000000 INFO @ Tue, 16 Jun 2020 08:21:08: 3000000 INFO @ Tue, 16 Jun 2020 08:21:09: 13000000 INFO @ Tue, 16 Jun 2020 08:21:12: 9000000 INFO @ Tue, 16 Jun 2020 08:21:14: 4000000 INFO @ Tue, 16 Jun 2020 08:21:16: 14000000 INFO @ Tue, 16 Jun 2020 08:21:18: 10000000 INFO @ Tue, 16 Jun 2020 08:21:21: 5000000 INFO @ Tue, 16 Jun 2020 08:21:23: 15000000 INFO @ Tue, 16 Jun 2020 08:21:24: 11000000 INFO @ Tue, 16 Jun 2020 08:21:27: 6000000 INFO @ Tue, 16 Jun 2020 08:21:29: 16000000 INFO @ Tue, 16 Jun 2020 08:21:29: 12000000 INFO @ Tue, 16 Jun 2020 08:21:33: 7000000 INFO @ Tue, 16 Jun 2020 08:21:35: 13000000 INFO @ Tue, 16 Jun 2020 08:21:36: 17000000 INFO @ Tue, 16 Jun 2020 08:21:40: 8000000 INFO @ Tue, 16 Jun 2020 08:21:41: 14000000 INFO @ Tue, 16 Jun 2020 08:21:42: 18000000 INFO @ Tue, 16 Jun 2020 08:21:46: 9000000 INFO @ Tue, 16 Jun 2020 08:21:47: 15000000 INFO @ Tue, 16 Jun 2020 08:21:49: 19000000 INFO @ Tue, 16 Jun 2020 08:21:52: 10000000 INFO @ Tue, 16 Jun 2020 08:21:53: 16000000 INFO @ Tue, 16 Jun 2020 08:21:55: 20000000 INFO @ Tue, 16 Jun 2020 08:21:59: 11000000 INFO @ Tue, 16 Jun 2020 08:21:59: 17000000 INFO @ Tue, 16 Jun 2020 08:22:01: 21000000 INFO @ Tue, 16 Jun 2020 08:22:05: 18000000 INFO @ Tue, 16 Jun 2020 08:22:05: 12000000 INFO @ Tue, 16 Jun 2020 08:22:07: 22000000 INFO @ Tue, 16 Jun 2020 08:22:11: 19000000 INFO @ Tue, 16 Jun 2020 08:22:11: 13000000 INFO @ Tue, 16 Jun 2020 08:22:13: 23000000 INFO @ Tue, 16 Jun 2020 08:22:17: 20000000 INFO @ Tue, 16 Jun 2020 08:22:18: 14000000 INFO @ Tue, 16 Jun 2020 08:22:20: 24000000 INFO @ Tue, 16 Jun 2020 08:22:23: 21000000 INFO @ Tue, 16 Jun 2020 08:22:24: 15000000 INFO @ Tue, 16 Jun 2020 08:22:26: 25000000 INFO @ Tue, 16 Jun 2020 08:22:29: 22000000 INFO @ Tue, 16 Jun 2020 08:22:30: 16000000 INFO @ Tue, 16 Jun 2020 08:22:32: 26000000 INFO @ Tue, 16 Jun 2020 08:22:35: 23000000 INFO @ Tue, 16 Jun 2020 08:22:36: 17000000 INFO @ Tue, 16 Jun 2020 08:22:39: 27000000 INFO @ Tue, 16 Jun 2020 08:22:41: 24000000 INFO @ Tue, 16 Jun 2020 08:22:43: 18000000 INFO @ Tue, 16 Jun 2020 08:22:45: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:47: 25000000 INFO @ Tue, 16 Jun 2020 08:22:49: 19000000 INFO @ Tue, 16 Jun 2020 08:22:52: 29000000 INFO @ Tue, 16 Jun 2020 08:22:53: 26000000 INFO @ Tue, 16 Jun 2020 08:22:55: 20000000 INFO @ Tue, 16 Jun 2020 08:22:58: 30000000 INFO @ Tue, 16 Jun 2020 08:22:58: 27000000 INFO @ Tue, 16 Jun 2020 08:23:01: 21000000 INFO @ Tue, 16 Jun 2020 08:23:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:04: #1 total tags in treatment: 30951768 INFO @ Tue, 16 Jun 2020 08:23:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:23:04: 28000000 INFO @ Tue, 16 Jun 2020 08:23:05: #1 tags after filtering in treatment: 30951768 INFO @ Tue, 16 Jun 2020 08:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:07: #2 number of paired peaks: 717 WARNING @ Tue, 16 Jun 2020 08:23:07: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:07: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 08:23:07: #2 alternative fragment length(s) may be 2,139,157,172,200,243 bps INFO @ Tue, 16 Jun 2020 08:23:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.05_model.r INFO @ Tue, 16 Jun 2020 08:23:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:07: 22000000 INFO @ Tue, 16 Jun 2020 08:23:10: 29000000 INFO @ Tue, 16 Jun 2020 08:23:13: 23000000 INFO @ Tue, 16 Jun 2020 08:23:16: 30000000 INFO @ Tue, 16 Jun 2020 08:23:19: 24000000 INFO @ Tue, 16 Jun 2020 08:23:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:22: #1 total tags in treatment: 30951768 INFO @ Tue, 16 Jun 2020 08:23:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:23:23: #1 tags after filtering in treatment: 30951768 INFO @ Tue, 16 Jun 2020 08:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:25: #2 number of paired peaks: 717 WARNING @ Tue, 16 Jun 2020 08:23:25: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:25: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 08:23:25: #2 alternative fragment length(s) may be 2,139,157,172,200,243 bps INFO @ Tue, 16 Jun 2020 08:23:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.10_model.r INFO @ Tue, 16 Jun 2020 08:23:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:23:25: 25000000 INFO @ Tue, 16 Jun 2020 08:23:31: 26000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:37: 27000000 INFO @ Tue, 16 Jun 2020 08:23:43: 28000000 INFO @ Tue, 16 Jun 2020 08:23:49: 29000000 INFO @ Tue, 16 Jun 2020 08:23:54: 30000000 INFO @ Tue, 16 Jun 2020 08:24:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:24:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:24:00: #1 total tags in treatment: 30951768 INFO @ Tue, 16 Jun 2020 08:24:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:24:01: #1 tags after filtering in treatment: 30951768 INFO @ Tue, 16 Jun 2020 08:24:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:03: #2 number of paired peaks: 717 WARNING @ Tue, 16 Jun 2020 08:24:03: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:03: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 08:24:03: #2 alternative fragment length(s) may be 2,139,157,172,200,243 bps INFO @ Tue, 16 Jun 2020 08:24:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.20_model.r INFO @ Tue, 16 Jun 2020 08:24:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:24:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:43: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (12062 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.10_summits.bed INFO @ Tue, 16 Jun 2020 08:25:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7139 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:25:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674100/SRX1674100.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3205 records, 4 fields): 4 millis CompletedMACS2peakCalling