Job ID = 6507789 SRX = SRX4085366 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:06:46 prefetch.2.10.7: 1) Downloading 'SRR7167395'... 2020-06-26T13:06:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:11:16 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:11:16 prefetch.2.10.7: 1) 'SRR7167395' was downloaded successfully Read 25802778 spots for SRR7167395/SRR7167395.sra Written 25802778 spots for SRR7167395/SRR7167395.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: 00:19:59 25802778 reads; of these: 25802778 (100.00%) were paired; of these: 8088315 (31.35%) aligned concordantly 0 times 15209827 (58.95%) aligned concordantly exactly 1 time 2504636 (9.71%) aligned concordantly >1 times ---- 8088315 pairs aligned concordantly 0 times; of these: 221227 (2.74%) aligned discordantly 1 time ---- 7867088 pairs aligned 0 times concordantly or discordantly; of these: 15734176 mates make up the pairs; of these: 13067675 (83.05%) aligned 0 times 2299548 (14.61%) aligned exactly 1 time 366953 (2.33%) aligned >1 times 74.68% overall alignment rate Time searching: 00:19:59 Overall time: 00:19:59 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] 4846842 / 17852277 = 0.2715 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 22:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.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 22:45:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:45:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:45:17: 1000000 INFO @ Fri, 26 Jun 2020 22:45:23: 2000000 INFO @ Fri, 26 Jun 2020 22:45:28: 3000000 INFO @ Fri, 26 Jun 2020 22:45:34: 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 22:45:39: 5000000 INFO @ Fri, 26 Jun 2020 22:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.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 22:45:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:45:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:45:45: 6000000 INFO @ Fri, 26 Jun 2020 22:45:47: 1000000 INFO @ Fri, 26 Jun 2020 22:45:51: 7000000 INFO @ Fri, 26 Jun 2020 22:45:54: 2000000 INFO @ Fri, 26 Jun 2020 22:45:57: 8000000 INFO @ Fri, 26 Jun 2020 22:46:00: 3000000 INFO @ Fri, 26 Jun 2020 22:46:03: 9000000 INFO @ Fri, 26 Jun 2020 22:46:06: 4000000 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 22:46:10: 10000000 INFO @ Fri, 26 Jun 2020 22:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.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 22:46:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:46:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:46:12: 5000000 INFO @ Fri, 26 Jun 2020 22:46:16: 11000000 INFO @ Fri, 26 Jun 2020 22:46:18: 1000000 INFO @ Fri, 26 Jun 2020 22:46:18: 6000000 INFO @ Fri, 26 Jun 2020 22:46:22: 12000000 INFO @ Fri, 26 Jun 2020 22:46:24: 7000000 INFO @ Fri, 26 Jun 2020 22:46:24: 2000000 INFO @ Fri, 26 Jun 2020 22:46:28: 13000000 INFO @ Fri, 26 Jun 2020 22:46:31: 8000000 INFO @ Fri, 26 Jun 2020 22:46:31: 3000000 INFO @ Fri, 26 Jun 2020 22:46:35: 14000000 INFO @ Fri, 26 Jun 2020 22:46:37: 9000000 INFO @ Fri, 26 Jun 2020 22:46:37: 4000000 INFO @ Fri, 26 Jun 2020 22:46:41: 15000000 INFO @ Fri, 26 Jun 2020 22:46:43: 10000000 INFO @ Fri, 26 Jun 2020 22:46:44: 5000000 INFO @ Fri, 26 Jun 2020 22:46:47: 16000000 INFO @ Fri, 26 Jun 2020 22:46:50: 11000000 INFO @ Fri, 26 Jun 2020 22:46:50: 6000000 INFO @ Fri, 26 Jun 2020 22:46:53: 17000000 INFO @ Fri, 26 Jun 2020 22:46:56: 12000000 INFO @ Fri, 26 Jun 2020 22:46:56: 7000000 INFO @ Fri, 26 Jun 2020 22:46:59: 18000000 INFO @ Fri, 26 Jun 2020 22:47:02: 13000000 INFO @ Fri, 26 Jun 2020 22:47:03: 8000000 INFO @ Fri, 26 Jun 2020 22:47:06: 19000000 INFO @ Fri, 26 Jun 2020 22:47:09: 14000000 INFO @ Fri, 26 Jun 2020 22:47:09: 9000000 INFO @ Fri, 26 Jun 2020 22:47:12: 20000000 INFO @ Fri, 26 Jun 2020 22:47:15: 15000000 INFO @ Fri, 26 Jun 2020 22:47:15: 10000000 INFO @ Fri, 26 Jun 2020 22:47:18: 21000000 INFO @ Fri, 26 Jun 2020 22:47:21: 16000000 INFO @ Fri, 26 Jun 2020 22:47:22: 11000000 INFO @ Fri, 26 Jun 2020 22:47:25: 22000000 INFO @ Fri, 26 Jun 2020 22:47:27: 17000000 INFO @ Fri, 26 Jun 2020 22:47:28: 12000000 INFO @ Fri, 26 Jun 2020 22:47:31: 23000000 INFO @ Fri, 26 Jun 2020 22:47:33: 18000000 INFO @ Fri, 26 Jun 2020 22:47:34: 13000000 INFO @ Fri, 26 Jun 2020 22:47:38: 24000000 INFO @ Fri, 26 Jun 2020 22:47:40: 19000000 INFO @ Fri, 26 Jun 2020 22:47:41: 14000000 INFO @ Fri, 26 Jun 2020 22:47:44: 25000000 INFO @ Fri, 26 Jun 2020 22:47:46: 20000000 INFO @ Fri, 26 Jun 2020 22:47:47: 15000000 INFO @ Fri, 26 Jun 2020 22:47:50: 26000000 INFO @ Fri, 26 Jun 2020 22:47:52: 21000000 INFO @ Fri, 26 Jun 2020 22:47:53: 16000000 INFO @ Fri, 26 Jun 2020 22:47:56: 27000000 INFO @ Fri, 26 Jun 2020 22:47:59: 22000000 INFO @ Fri, 26 Jun 2020 22:47:59: 17000000 INFO @ Fri, 26 Jun 2020 22:48:03: 28000000 INFO @ Fri, 26 Jun 2020 22:48:05: 23000000 INFO @ Fri, 26 Jun 2020 22:48:05: 18000000 INFO @ Fri, 26 Jun 2020 22:48:08: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:48:08: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:48:08: #1 total tags in treatment: 12902313 INFO @ Fri, 26 Jun 2020 22:48:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:48:08: #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 22:48:08: #1 tags after filtering in treatment: 11759628 INFO @ Fri, 26 Jun 2020 22:48:08: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:48:08: #1 finished! INFO @ Fri, 26 Jun 2020 22:48:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:48:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:48:09: #2 number of paired peaks: 310 WARNING @ Fri, 26 Jun 2020 22:48:09: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Fri, 26 Jun 2020 22:48:09: start model_add_line... INFO @ Fri, 26 Jun 2020 22:48:09: start X-correlation... INFO @ Fri, 26 Jun 2020 22:48:09: end of X-cor INFO @ Fri, 26 Jun 2020 22:48:09: #2 finished! INFO @ Fri, 26 Jun 2020 22:48:09: #2 predicted fragment length is 118 bps INFO @ Fri, 26 Jun 2020 22:48:09: #2 alternative fragment length(s) may be 4,118 bps INFO @ Fri, 26 Jun 2020 22:48:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.05_model.r INFO @ Fri, 26 Jun 2020 22:48:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:48:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:48:11: 24000000 INFO @ Fri, 26 Jun 2020 22:48:11: 19000000 INFO @ Fri, 26 Jun 2020 22:48:17: 25000000 INFO @ Fri, 26 Jun 2020 22:48:18: 20000000 INFO @ Fri, 26 Jun 2020 22:48:24: 26000000 INFO @ Fri, 26 Jun 2020 22:48:24: 21000000 INFO @ Fri, 26 Jun 2020 22:48:30: 27000000 INFO @ Fri, 26 Jun 2020 22:48:30: 22000000 INFO @ Fri, 26 Jun 2020 22:48:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:48:36: 28000000 INFO @ Fri, 26 Jun 2020 22:48:37: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:48:42: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:48:42: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:48:42: #1 total tags in treatment: 12902313 INFO @ Fri, 26 Jun 2020 22:48:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:48:42: #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 22:48:42: #1 tags after filtering in treatment: 11759628 INFO @ Fri, 26 Jun 2020 22:48:42: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:48:42: #1 finished! INFO @ Fri, 26 Jun 2020 22:48:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:48:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:48:43: #2 number of paired peaks: 310 WARNING @ Fri, 26 Jun 2020 22:48:43: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Fri, 26 Jun 2020 22:48:43: start model_add_line... INFO @ Fri, 26 Jun 2020 22:48:43: start X-correlation... INFO @ Fri, 26 Jun 2020 22:48:43: end of X-cor INFO @ Fri, 26 Jun 2020 22:48:43: #2 finished! INFO @ Fri, 26 Jun 2020 22:48:43: #2 predicted fragment length is 118 bps INFO @ Fri, 26 Jun 2020 22:48:43: #2 alternative fragment length(s) may be 4,118 bps INFO @ Fri, 26 Jun 2020 22:48:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.10_model.r INFO @ Fri, 26 Jun 2020 22:48:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:48:43: 24000000 INFO @ Fri, 26 Jun 2020 22:48:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:48:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:48:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.05_summits.bed INFO @ Fri, 26 Jun 2020 22:48:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (971 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:48:49: 25000000 INFO @ Fri, 26 Jun 2020 22:48:55: 26000000 INFO @ Fri, 26 Jun 2020 22:49:01: 27000000 INFO @ Fri, 26 Jun 2020 22:49:07: 28000000 INFO @ Fri, 26 Jun 2020 22:49:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:49:11: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:49:11: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:49:11: #1 total tags in treatment: 12902313 INFO @ Fri, 26 Jun 2020 22:49:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:49:11: #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 22:49:12: #1 tags after filtering in treatment: 11759628 INFO @ Fri, 26 Jun 2020 22:49:12: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 22:49:12: #1 finished! INFO @ Fri, 26 Jun 2020 22:49:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:49:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:49:13: #2 number of paired peaks: 310 WARNING @ Fri, 26 Jun 2020 22:49:13: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Fri, 26 Jun 2020 22:49:13: start model_add_line... INFO @ Fri, 26 Jun 2020 22:49:13: start X-correlation... INFO @ Fri, 26 Jun 2020 22:49:13: end of X-cor INFO @ Fri, 26 Jun 2020 22:49:13: #2 finished! INFO @ Fri, 26 Jun 2020 22:49:13: #2 predicted fragment length is 118 bps INFO @ Fri, 26 Jun 2020 22:49:13: #2 alternative fragment length(s) may be 4,118 bps INFO @ Fri, 26 Jun 2020 22:49:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.20_model.r INFO @ Fri, 26 Jun 2020 22:49:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:49:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:49:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:49:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:49:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.10_summits.bed INFO @ Fri, 26 Jun 2020 22:49:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (579 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:49:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:49:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:49:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:49:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085366/SRX4085366.20_summits.bed INFO @ Fri, 26 Jun 2020 22:49:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (291 records, 4 fields): 1 millis CompletedMACS2peakCalling