Job ID = 6366514 SRX = SRX1674094 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:37 prefetch.2.10.7: 1) Downloading 'SRR3320140'... 2020-06-15T22:46:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:36 prefetch.2.10.7: 1) 'SRR3320140' was downloaded successfully Read 56496066 spots for SRR3320140/SRR3320140.sra Written 56496066 spots for SRR3320140/SRR3320140.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: 00:12:19 56496066 reads; of these: 56496066 (100.00%) were unpaired; of these: 1304567 (2.31%) aligned 0 times 49346158 (87.34%) aligned exactly 1 time 5845341 (10.35%) aligned >1 times 97.69% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:19 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] 23269524 / 55191499 = 0.4216 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 08:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.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 08:14:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:20: 1000000 INFO @ Tue, 16 Jun 2020 08:14:24: 2000000 INFO @ Tue, 16 Jun 2020 08:14:29: 3000000 INFO @ Tue, 16 Jun 2020 08:14:34: 4000000 INFO @ Tue, 16 Jun 2020 08:14:39: 5000000 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 08:14:44: 6000000 INFO @ Tue, 16 Jun 2020 08:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.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 08:14:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:50: 7000000 INFO @ Tue, 16 Jun 2020 08:14:50: 1000000 INFO @ Tue, 16 Jun 2020 08:14:55: 8000000 INFO @ Tue, 16 Jun 2020 08:14:56: 2000000 INFO @ Tue, 16 Jun 2020 08:15:01: 9000000 INFO @ Tue, 16 Jun 2020 08:15:01: 3000000 INFO @ Tue, 16 Jun 2020 08:15:06: 10000000 INFO @ Tue, 16 Jun 2020 08:15:07: 4000000 INFO @ Tue, 16 Jun 2020 08:15:12: 11000000 INFO @ Tue, 16 Jun 2020 08:15:12: 5000000 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 08:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.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 08:15:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:17: 12000000 INFO @ Tue, 16 Jun 2020 08:15:18: 6000000 INFO @ Tue, 16 Jun 2020 08:15:20: 1000000 INFO @ Tue, 16 Jun 2020 08:15:23: 13000000 INFO @ Tue, 16 Jun 2020 08:15:23: 7000000 INFO @ Tue, 16 Jun 2020 08:15:26: 2000000 INFO @ Tue, 16 Jun 2020 08:15:28: 14000000 INFO @ Tue, 16 Jun 2020 08:15:29: 8000000 INFO @ Tue, 16 Jun 2020 08:15:32: 3000000 INFO @ Tue, 16 Jun 2020 08:15:34: 15000000 INFO @ Tue, 16 Jun 2020 08:15:34: 9000000 INFO @ Tue, 16 Jun 2020 08:15:37: 4000000 INFO @ Tue, 16 Jun 2020 08:15:39: 16000000 INFO @ Tue, 16 Jun 2020 08:15:40: 10000000 INFO @ Tue, 16 Jun 2020 08:15:43: 5000000 INFO @ Tue, 16 Jun 2020 08:15:44: 17000000 INFO @ Tue, 16 Jun 2020 08:15:45: 11000000 INFO @ Tue, 16 Jun 2020 08:15:48: 6000000 INFO @ Tue, 16 Jun 2020 08:15:50: 18000000 INFO @ Tue, 16 Jun 2020 08:15:51: 12000000 INFO @ Tue, 16 Jun 2020 08:15:53: 7000000 INFO @ Tue, 16 Jun 2020 08:15:55: 19000000 INFO @ Tue, 16 Jun 2020 08:15:56: 13000000 INFO @ Tue, 16 Jun 2020 08:15:58: 8000000 INFO @ Tue, 16 Jun 2020 08:16:01: 20000000 INFO @ Tue, 16 Jun 2020 08:16:01: 14000000 INFO @ Tue, 16 Jun 2020 08:16:04: 9000000 INFO @ Tue, 16 Jun 2020 08:16:06: 21000000 INFO @ Tue, 16 Jun 2020 08:16:07: 15000000 INFO @ Tue, 16 Jun 2020 08:16:09: 10000000 INFO @ Tue, 16 Jun 2020 08:16:11: 22000000 INFO @ Tue, 16 Jun 2020 08:16:12: 16000000 INFO @ Tue, 16 Jun 2020 08:16:14: 11000000 INFO @ Tue, 16 Jun 2020 08:16:17: 23000000 INFO @ Tue, 16 Jun 2020 08:16:18: 17000000 INFO @ Tue, 16 Jun 2020 08:16:20: 12000000 INFO @ Tue, 16 Jun 2020 08:16:22: 24000000 INFO @ Tue, 16 Jun 2020 08:16:23: 18000000 INFO @ Tue, 16 Jun 2020 08:16:25: 13000000 INFO @ Tue, 16 Jun 2020 08:16:27: 25000000 INFO @ Tue, 16 Jun 2020 08:16:28: 19000000 INFO @ Tue, 16 Jun 2020 08:16:30: 14000000 INFO @ Tue, 16 Jun 2020 08:16:33: 26000000 INFO @ Tue, 16 Jun 2020 08:16:34: 20000000 INFO @ Tue, 16 Jun 2020 08:16:36: 15000000 INFO @ Tue, 16 Jun 2020 08:16:38: 27000000 INFO @ Tue, 16 Jun 2020 08:16:39: 21000000 INFO @ Tue, 16 Jun 2020 08:16:41: 16000000 INFO @ Tue, 16 Jun 2020 08:16:43: 28000000 INFO @ Tue, 16 Jun 2020 08:16:44: 22000000 INFO @ Tue, 16 Jun 2020 08:16:46: 17000000 INFO @ Tue, 16 Jun 2020 08:16:49: 29000000 INFO @ Tue, 16 Jun 2020 08:16:50: 23000000 INFO @ Tue, 16 Jun 2020 08:16:51: 18000000 INFO @ Tue, 16 Jun 2020 08:16:54: 30000000 INFO @ Tue, 16 Jun 2020 08:16:55: 24000000 INFO @ Tue, 16 Jun 2020 08:16:57: 19000000 INFO @ Tue, 16 Jun 2020 08:16:59: 31000000 INFO @ Tue, 16 Jun 2020 08:17:00: 25000000 INFO @ Tue, 16 Jun 2020 08:17:02: 20000000 INFO @ Tue, 16 Jun 2020 08:17:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:17:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:17:04: #1 total tags in treatment: 31921975 INFO @ Tue, 16 Jun 2020 08:17:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:04: #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 08:17:05: #1 tags after filtering in treatment: 31921975 INFO @ Tue, 16 Jun 2020 08:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:06: 26000000 INFO @ Tue, 16 Jun 2020 08:17:07: #2 number of paired peaks: 159 WARNING @ Tue, 16 Jun 2020 08:17:07: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:07: 21000000 INFO @ Tue, 16 Jun 2020 08:17:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:07: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 08:17:07: #2 alternative fragment length(s) may be 2,95,144,177,198,225,236,257,273,306,344,417,512 bps INFO @ Tue, 16 Jun 2020 08:17:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.05_model.r INFO @ Tue, 16 Jun 2020 08:17:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:11: 27000000 INFO @ Tue, 16 Jun 2020 08:17:12: 22000000 INFO @ Tue, 16 Jun 2020 08:17:16: 28000000 INFO @ Tue, 16 Jun 2020 08:17:17: 23000000 INFO @ Tue, 16 Jun 2020 08:17:21: 29000000 INFO @ Tue, 16 Jun 2020 08:17:22: 24000000 INFO @ Tue, 16 Jun 2020 08:17:27: 30000000 INFO @ Tue, 16 Jun 2020 08:17:28: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:17:32: 31000000 INFO @ Tue, 16 Jun 2020 08:17:33: 26000000 INFO @ Tue, 16 Jun 2020 08:17:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:17:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:17:37: #1 total tags in treatment: 31921975 INFO @ Tue, 16 Jun 2020 08:17:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:37: #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 08:17:38: #1 tags after filtering in treatment: 31921975 INFO @ Tue, 16 Jun 2020 08:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:39: 27000000 INFO @ Tue, 16 Jun 2020 08:17:40: #2 number of paired peaks: 159 WARNING @ Tue, 16 Jun 2020 08:17:40: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:40: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 08:17:40: #2 alternative fragment length(s) may be 2,95,144,177,198,225,236,257,273,306,344,417,512 bps INFO @ Tue, 16 Jun 2020 08:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.10_model.r INFO @ Tue, 16 Jun 2020 08:17:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:44: 28000000 INFO @ Tue, 16 Jun 2020 08:17:49: 29000000 INFO @ Tue, 16 Jun 2020 08:17:54: 30000000 INFO @ Tue, 16 Jun 2020 08:18:00: 31000000 INFO @ Tue, 16 Jun 2020 08:18:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:05: #1 total tags in treatment: 31921975 INFO @ Tue, 16 Jun 2020 08:18:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:05: #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 08:18:05: #1 tags after filtering in treatment: 31921975 INFO @ Tue, 16 Jun 2020 08:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:07: #2 number of paired peaks: 159 WARNING @ Tue, 16 Jun 2020 08:18:07: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:08: #2 predicted fragment length is 177 bps INFO @ Tue, 16 Jun 2020 08:18:08: #2 alternative fragment length(s) may be 2,95,144,177,198,225,236,257,273,306,344,417,512 bps INFO @ Tue, 16 Jun 2020 08:18:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.20_model.r INFO @ Tue, 16 Jun 2020 08:18:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:18:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:45: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10162 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.10_summits.bed INFO @ Tue, 16 Jun 2020 08:19:17: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6688 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674094/SRX1674094.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3548 records, 4 fields): 5 millis CompletedMACS2peakCalling