Job ID = 6497348 SRX = SRX1995035 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:35:50 prefetch.2.10.7: 1) Downloading 'SRR3993967'... 2020-06-25T21:35:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:38:51 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:38:51 prefetch.2.10.7: 1) 'SRR3993967' was downloaded successfully Read 18653692 spots for SRR3993967/SRR3993967.sra Written 18653692 spots for SRR3993967/SRR3993967.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: 00:26:38 18653692 reads; of these: 18653692 (100.00%) were paired; of these: 1314967 (7.05%) aligned concordantly 0 times 11931998 (63.97%) aligned concordantly exactly 1 time 5406727 (28.98%) aligned concordantly >1 times ---- 1314967 pairs aligned concordantly 0 times; of these: 478121 (36.36%) aligned discordantly 1 time ---- 836846 pairs aligned 0 times concordantly or discordantly; of these: 1673692 mates make up the pairs; of these: 1106733 (66.13%) aligned 0 times 265294 (15.85%) aligned exactly 1 time 301665 (18.02%) aligned >1 times 97.03% overall alignment rate Time searching: 00:26:38 Overall time: 00:26:38 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_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] 3653394 / 17799736 = 0.2052 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 07:16:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.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 07:16:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:16:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:16:49: 1000000 INFO @ Fri, 26 Jun 2020 07:16:54: 2000000 INFO @ Fri, 26 Jun 2020 07:16:59: 3000000 INFO @ Fri, 26 Jun 2020 07:17:04: 4000000 INFO @ Fri, 26 Jun 2020 07:17:09: 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 @ Fri, 26 Jun 2020 07:17:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.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 07:17:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:17:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:17:14: 6000000 INFO @ Fri, 26 Jun 2020 07:17:19: 1000000 INFO @ Fri, 26 Jun 2020 07:17:19: 7000000 INFO @ Fri, 26 Jun 2020 07:17:25: 2000000 INFO @ Fri, 26 Jun 2020 07:17:25: 8000000 INFO @ Fri, 26 Jun 2020 07:17:30: 3000000 INFO @ Fri, 26 Jun 2020 07:17:31: 9000000 INFO @ Fri, 26 Jun 2020 07:17:36: 4000000 INFO @ Fri, 26 Jun 2020 07:17:36: 10000000 INFO @ Fri, 26 Jun 2020 07:17:41: 5000000 INFO @ Fri, 26 Jun 2020 07:17:42: 11000000 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 07:17:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.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 07:17:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:17:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:17:47: 6000000 INFO @ Fri, 26 Jun 2020 07:17:47: 12000000 INFO @ Fri, 26 Jun 2020 07:17:50: 1000000 INFO @ Fri, 26 Jun 2020 07:17:54: 7000000 INFO @ Fri, 26 Jun 2020 07:17:54: 13000000 INFO @ Fri, 26 Jun 2020 07:17:57: 2000000 INFO @ Fri, 26 Jun 2020 07:18:00: 8000000 INFO @ Fri, 26 Jun 2020 07:18:00: 14000000 INFO @ Fri, 26 Jun 2020 07:18:04: 3000000 INFO @ Fri, 26 Jun 2020 07:18:06: 9000000 INFO @ Fri, 26 Jun 2020 07:18:06: 15000000 INFO @ Fri, 26 Jun 2020 07:18:11: 4000000 INFO @ Fri, 26 Jun 2020 07:18:13: 10000000 INFO @ Fri, 26 Jun 2020 07:18:13: 16000000 INFO @ Fri, 26 Jun 2020 07:18:17: 5000000 INFO @ Fri, 26 Jun 2020 07:18:19: 11000000 INFO @ Fri, 26 Jun 2020 07:18:19: 17000000 INFO @ Fri, 26 Jun 2020 07:18:24: 6000000 INFO @ Fri, 26 Jun 2020 07:18:25: 12000000 INFO @ Fri, 26 Jun 2020 07:18:26: 18000000 INFO @ Fri, 26 Jun 2020 07:18:30: 7000000 INFO @ Fri, 26 Jun 2020 07:18:31: 13000000 INFO @ Fri, 26 Jun 2020 07:18:32: 19000000 INFO @ Fri, 26 Jun 2020 07:18:37: 8000000 INFO @ Fri, 26 Jun 2020 07:18:37: 14000000 INFO @ Fri, 26 Jun 2020 07:18:38: 20000000 INFO @ Fri, 26 Jun 2020 07:18:43: 15000000 INFO @ Fri, 26 Jun 2020 07:18:44: 9000000 INFO @ Fri, 26 Jun 2020 07:18:44: 21000000 INFO @ Fri, 26 Jun 2020 07:18:50: 16000000 INFO @ Fri, 26 Jun 2020 07:18:50: 22000000 INFO @ Fri, 26 Jun 2020 07:18:50: 10000000 INFO @ Fri, 26 Jun 2020 07:18:56: 17000000 INFO @ Fri, 26 Jun 2020 07:18:56: 23000000 INFO @ Fri, 26 Jun 2020 07:18:57: 11000000 INFO @ Fri, 26 Jun 2020 07:19:02: 18000000 INFO @ Fri, 26 Jun 2020 07:19:02: 24000000 INFO @ Fri, 26 Jun 2020 07:19:04: 12000000 INFO @ Fri, 26 Jun 2020 07:19:08: 19000000 INFO @ Fri, 26 Jun 2020 07:19:09: 25000000 INFO @ Fri, 26 Jun 2020 07:19:11: 13000000 INFO @ Fri, 26 Jun 2020 07:19:14: 20000000 INFO @ Fri, 26 Jun 2020 07:19:15: 26000000 INFO @ Fri, 26 Jun 2020 07:19:17: 14000000 INFO @ Fri, 26 Jun 2020 07:19:20: 21000000 INFO @ Fri, 26 Jun 2020 07:19:21: 27000000 INFO @ Fri, 26 Jun 2020 07:19:24: 15000000 INFO @ Fri, 26 Jun 2020 07:19:26: 22000000 INFO @ Fri, 26 Jun 2020 07:19:27: 28000000 INFO @ Fri, 26 Jun 2020 07:19:31: 16000000 INFO @ Fri, 26 Jun 2020 07:19:32: 23000000 INFO @ Fri, 26 Jun 2020 07:19:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:19:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:19:33: #1 total tags in treatment: 13726007 INFO @ Fri, 26 Jun 2020 07:19:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:19:33: #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 07:19:33: #1 tags after filtering in treatment: 10799697 INFO @ Fri, 26 Jun 2020 07:19:33: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 07:19:33: #1 finished! INFO @ Fri, 26 Jun 2020 07:19:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:19:34: #2 number of paired peaks: 1972 INFO @ Fri, 26 Jun 2020 07:19:34: start model_add_line... INFO @ Fri, 26 Jun 2020 07:19:34: start X-correlation... INFO @ Fri, 26 Jun 2020 07:19:34: end of X-cor INFO @ Fri, 26 Jun 2020 07:19:34: #2 finished! INFO @ Fri, 26 Jun 2020 07:19:34: #2 predicted fragment length is 183 bps INFO @ Fri, 26 Jun 2020 07:19:34: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 26 Jun 2020 07:19:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.05_model.r INFO @ Fri, 26 Jun 2020 07:19:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:19:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:19:37: 17000000 INFO @ Fri, 26 Jun 2020 07:19:38: 24000000 INFO @ Fri, 26 Jun 2020 07:19:44: 18000000 INFO @ Fri, 26 Jun 2020 07:19:45: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:19:51: 19000000 INFO @ Fri, 26 Jun 2020 07:19:51: 26000000 INFO @ Fri, 26 Jun 2020 07:19:57: 27000000 INFO @ Fri, 26 Jun 2020 07:19:57: 20000000 INFO @ Fri, 26 Jun 2020 07:20:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:03: 28000000 INFO @ Fri, 26 Jun 2020 07:20:04: 21000000 INFO @ Fri, 26 Jun 2020 07:20:08: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:20:08: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:20:08: #1 total tags in treatment: 13726007 INFO @ Fri, 26 Jun 2020 07:20:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:08: #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 07:20:08: #1 tags after filtering in treatment: 10799697 INFO @ Fri, 26 Jun 2020 07:20:08: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 07:20:08: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:09: #2 number of paired peaks: 1972 INFO @ Fri, 26 Jun 2020 07:20:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:09: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:09: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:09: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:09: #2 predicted fragment length is 183 bps INFO @ Fri, 26 Jun 2020 07:20:09: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 26 Jun 2020 07:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.10_model.r INFO @ Fri, 26 Jun 2020 07:20:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:20:11: 22000000 INFO @ Fri, 26 Jun 2020 07:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.05_summits.bed INFO @ Fri, 26 Jun 2020 07:20:15: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4371 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:20:17: 23000000 INFO @ Fri, 26 Jun 2020 07:20:23: 24000000 INFO @ Fri, 26 Jun 2020 07:20:30: 25000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:20:36: 26000000 INFO @ Fri, 26 Jun 2020 07:20:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:42: 27000000 INFO @ Fri, 26 Jun 2020 07:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:49: 28000000 INFO @ Fri, 26 Jun 2020 07:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.10_summits.bed INFO @ Fri, 26 Jun 2020 07:20:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2810 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:20:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:20:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:20:54: #1 total tags in treatment: 13726007 INFO @ Fri, 26 Jun 2020 07:20:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:54: #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 07:20:54: #1 tags after filtering in treatment: 10799697 INFO @ Fri, 26 Jun 2020 07:20:54: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 07:20:54: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:55: #2 number of paired peaks: 1972 INFO @ Fri, 26 Jun 2020 07:20:55: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:55: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:55: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:55: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:55: #2 predicted fragment length is 183 bps INFO @ Fri, 26 Jun 2020 07:20:55: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 26 Jun 2020 07:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.20_model.r INFO @ Fri, 26 Jun 2020 07:20:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:21:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1995035/SRX1995035.20_summits.bed INFO @ Fri, 26 Jun 2020 07:21:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 3 millis CompletedMACS2peakCalling