Job ID = 6507723 SRX = SRX1353663 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T12:41:31 prefetch.2.10.7: 1) Downloading 'SRR2722817'... 2020-06-26T12:41:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:43:03 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:43:03 prefetch.2.10.7: 1) 'SRR2722817' was downloaded successfully Read 14006131 spots for SRR2722817/SRR2722817.sra Written 14006131 spots for SRR2722817/SRR2722817.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:54 14006131 reads; of these: 14006131 (100.00%) were paired; of these: 1032760 (7.37%) aligned concordantly 0 times 10679710 (76.25%) aligned concordantly exactly 1 time 2293661 (16.38%) aligned concordantly >1 times ---- 1032760 pairs aligned concordantly 0 times; of these: 276583 (26.78%) aligned discordantly 1 time ---- 756177 pairs aligned 0 times concordantly or discordantly; of these: 1512354 mates make up the pairs; of these: 1074439 (71.04%) aligned 0 times 269240 (17.80%) aligned exactly 1 time 168675 (11.15%) aligned >1 times 96.16% overall alignment rate Time searching: 00:15:55 Overall time: 00:15:55 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 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 290398 / 13199576 = 0.0220 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 @ Fri, 26 Jun 2020 22:10:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.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 @ Fri, 26 Jun 2020 22:10:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:10:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:10:37: 1000000 INFO @ Fri, 26 Jun 2020 22:10:43: 2000000 INFO @ Fri, 26 Jun 2020 22:10:49: 3000000 INFO @ Fri, 26 Jun 2020 22:10:56: 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 @ Fri, 26 Jun 2020 22:11:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.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 @ Fri, 26 Jun 2020 22:11:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:11:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:11:02: 5000000 INFO @ Fri, 26 Jun 2020 22:11:08: 1000000 INFO @ Fri, 26 Jun 2020 22:11:09: 6000000 INFO @ Fri, 26 Jun 2020 22:11:14: 2000000 INFO @ Fri, 26 Jun 2020 22:11:15: 7000000 INFO @ Fri, 26 Jun 2020 22:11:21: 3000000 INFO @ Fri, 26 Jun 2020 22:11:22: 8000000 INFO @ Fri, 26 Jun 2020 22:11:27: 4000000 INFO @ Fri, 26 Jun 2020 22:11:28: 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 @ Fri, 26 Jun 2020 22:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.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 @ Fri, 26 Jun 2020 22:11:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:11:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:11:34: 5000000 INFO @ Fri, 26 Jun 2020 22:11:35: 10000000 INFO @ Fri, 26 Jun 2020 22:11:38: 1000000 INFO @ Fri, 26 Jun 2020 22:11:41: 6000000 INFO @ Fri, 26 Jun 2020 22:11:43: 11000000 INFO @ Fri, 26 Jun 2020 22:11:45: 2000000 INFO @ Fri, 26 Jun 2020 22:11:48: 7000000 INFO @ Fri, 26 Jun 2020 22:11:49: 12000000 INFO @ Fri, 26 Jun 2020 22:11:51: 3000000 INFO @ Fri, 26 Jun 2020 22:11:55: 8000000 INFO @ Fri, 26 Jun 2020 22:11:56: 13000000 INFO @ Fri, 26 Jun 2020 22:11:58: 4000000 INFO @ Fri, 26 Jun 2020 22:12:01: 9000000 INFO @ Fri, 26 Jun 2020 22:12:04: 14000000 INFO @ Fri, 26 Jun 2020 22:12:05: 5000000 INFO @ Fri, 26 Jun 2020 22:12:08: 10000000 INFO @ Fri, 26 Jun 2020 22:12:11: 15000000 INFO @ Fri, 26 Jun 2020 22:12:12: 6000000 INFO @ Fri, 26 Jun 2020 22:12:15: 11000000 INFO @ Fri, 26 Jun 2020 22:12:18: 16000000 INFO @ Fri, 26 Jun 2020 22:12:19: 7000000 INFO @ Fri, 26 Jun 2020 22:12:22: 12000000 INFO @ Fri, 26 Jun 2020 22:12:25: 8000000 INFO @ Fri, 26 Jun 2020 22:12:26: 17000000 INFO @ Fri, 26 Jun 2020 22:12:29: 13000000 INFO @ Fri, 26 Jun 2020 22:12:32: 9000000 INFO @ Fri, 26 Jun 2020 22:12:33: 18000000 INFO @ Fri, 26 Jun 2020 22:12:35: 14000000 INFO @ Fri, 26 Jun 2020 22:12:39: 10000000 INFO @ Fri, 26 Jun 2020 22:12:40: 19000000 INFO @ Fri, 26 Jun 2020 22:12:42: 15000000 INFO @ Fri, 26 Jun 2020 22:12:46: 11000000 INFO @ Fri, 26 Jun 2020 22:12:47: 20000000 INFO @ Fri, 26 Jun 2020 22:12:49: 16000000 INFO @ Fri, 26 Jun 2020 22:12:53: 12000000 INFO @ Fri, 26 Jun 2020 22:12:54: 21000000 INFO @ Fri, 26 Jun 2020 22:12:56: 17000000 INFO @ Fri, 26 Jun 2020 22:13:00: 13000000 INFO @ Fri, 26 Jun 2020 22:13:00: 22000000 INFO @ Fri, 26 Jun 2020 22:13:03: 18000000 INFO @ Fri, 26 Jun 2020 22:13:07: 14000000 INFO @ Fri, 26 Jun 2020 22:13:07: 23000000 INFO @ Fri, 26 Jun 2020 22:13:10: 19000000 INFO @ Fri, 26 Jun 2020 22:13:13: 15000000 INFO @ Fri, 26 Jun 2020 22:13:15: 24000000 INFO @ Fri, 26 Jun 2020 22:13:16: 20000000 INFO @ Fri, 26 Jun 2020 22:13:20: 16000000 INFO @ Fri, 26 Jun 2020 22:13:22: 25000000 INFO @ Fri, 26 Jun 2020 22:13:23: 21000000 INFO @ Fri, 26 Jun 2020 22:13:27: 17000000 INFO @ Fri, 26 Jun 2020 22:13:29: 26000000 INFO @ Fri, 26 Jun 2020 22:13:30: 22000000 INFO @ Fri, 26 Jun 2020 22:13:31: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:13:31: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:13:31: #1 total tags in treatment: 12684698 INFO @ Fri, 26 Jun 2020 22:13:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:13:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:13:31: #1 tags after filtering in treatment: 11648744 INFO @ Fri, 26 Jun 2020 22:13:31: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 22:13:31: #1 finished! INFO @ Fri, 26 Jun 2020 22:13:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:13:32: #2 number of paired peaks: 360 WARNING @ Fri, 26 Jun 2020 22:13:32: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Fri, 26 Jun 2020 22:13:32: start model_add_line... INFO @ Fri, 26 Jun 2020 22:13:32: start X-correlation... INFO @ Fri, 26 Jun 2020 22:13:32: end of X-cor INFO @ Fri, 26 Jun 2020 22:13:32: #2 finished! INFO @ Fri, 26 Jun 2020 22:13:32: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 22:13:32: #2 alternative fragment length(s) may be 4,125 bps INFO @ Fri, 26 Jun 2020 22:13:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.05_model.r INFO @ Fri, 26 Jun 2020 22:13:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:13:34: 18000000 INFO @ Fri, 26 Jun 2020 22:13:37: 23000000 INFO @ Fri, 26 Jun 2020 22:13:40: 19000000 INFO @ Fri, 26 Jun 2020 22:13:43: 24000000 INFO @ Fri, 26 Jun 2020 22:13:46: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:13:49: 25000000 INFO @ Fri, 26 Jun 2020 22:13:53: 21000000 INFO @ Fri, 26 Jun 2020 22:13:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:13:56: 26000000 INFO @ Fri, 26 Jun 2020 22:13:58: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:13:58: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:13:58: #1 total tags in treatment: 12684698 INFO @ Fri, 26 Jun 2020 22:13:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:13:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:13:58: #1 tags after filtering in treatment: 11648744 INFO @ Fri, 26 Jun 2020 22:13:58: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 22:13:58: #1 finished! INFO @ Fri, 26 Jun 2020 22:13:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:13:59: 22000000 INFO @ Fri, 26 Jun 2020 22:13:59: #2 number of paired peaks: 360 WARNING @ Fri, 26 Jun 2020 22:13:59: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Fri, 26 Jun 2020 22:13:59: start model_add_line... INFO @ Fri, 26 Jun 2020 22:13:59: start X-correlation... INFO @ Fri, 26 Jun 2020 22:13:59: end of X-cor INFO @ Fri, 26 Jun 2020 22:13:59: #2 finished! INFO @ Fri, 26 Jun 2020 22:13:59: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 22:13:59: #2 alternative fragment length(s) may be 4,125 bps INFO @ Fri, 26 Jun 2020 22:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.10_model.r INFO @ Fri, 26 Jun 2020 22:13:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:14:05: 23000000 INFO @ Fri, 26 Jun 2020 22:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.05_summits.bed INFO @ Fri, 26 Jun 2020 22:14:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (569 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:14:11: 24000000 INFO @ Fri, 26 Jun 2020 22:14:17: 25000000 INFO @ Fri, 26 Jun 2020 22:14:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:14:23: 26000000 INFO @ Fri, 26 Jun 2020 22:14:25: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:14:25: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:14:25: #1 total tags in treatment: 12684698 INFO @ Fri, 26 Jun 2020 22:14:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:14:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:14:25: #1 tags after filtering in treatment: 11648744 INFO @ Fri, 26 Jun 2020 22:14:25: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 22:14:25: #1 finished! INFO @ Fri, 26 Jun 2020 22:14:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:14:26: #2 number of paired peaks: 360 WARNING @ Fri, 26 Jun 2020 22:14:26: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Fri, 26 Jun 2020 22:14:26: start model_add_line... INFO @ Fri, 26 Jun 2020 22:14:26: start X-correlation... INFO @ Fri, 26 Jun 2020 22:14:26: end of X-cor INFO @ Fri, 26 Jun 2020 22:14:26: #2 finished! INFO @ Fri, 26 Jun 2020 22:14:26: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 22:14:26: #2 alternative fragment length(s) may be 4,125 bps INFO @ Fri, 26 Jun 2020 22:14:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.20_model.r INFO @ Fri, 26 Jun 2020 22:14:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:14:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:14:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:14:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.10_summits.bed INFO @ Fri, 26 Jun 2020 22:14:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:14:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:14:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:14:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:14:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353663/SRX1353663.20_summits.bed INFO @ Fri, 26 Jun 2020 22:14:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 2 millis CompletedMACS2peakCalling