Job ID = 6368237 SRX = SRX494920 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:11:20 prefetch.2.10.7: 1) Downloading 'SRR1198452'... 2020-06-16T00:11:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:23 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:23 prefetch.2.10.7: 1) 'SRR1198452' was downloaded successfully Read 36072847 spots for SRR1198452/SRR1198452.sra Written 36072847 spots for SRR1198452/SRR1198452.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: 00:07:57 36072847 reads; of these: 36072847 (100.00%) were unpaired; of these: 1318777 (3.66%) aligned 0 times 31090920 (86.19%) aligned exactly 1 time 3663150 (10.15%) aligned >1 times 96.34% overall alignment rate Time searching: 00:07:57 Overall time: 00:07:57 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_rmdupse_core] 12956439 / 34754070 = 0.3728 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 09:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.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 09:33:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:04: 1000000 INFO @ Tue, 16 Jun 2020 09:34:12: 2000000 INFO @ Tue, 16 Jun 2020 09:34:19: 3000000 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 09:34:26: 4000000 INFO @ Tue, 16 Jun 2020 09:34:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.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 09:34:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:34: 5000000 INFO @ Tue, 16 Jun 2020 09:34:34: 1000000 INFO @ Tue, 16 Jun 2020 09:34:41: 2000000 INFO @ Tue, 16 Jun 2020 09:34:41: 6000000 INFO @ Tue, 16 Jun 2020 09:34:48: 3000000 INFO @ Tue, 16 Jun 2020 09:34:49: 7000000 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 09:34:56: 4000000 INFO @ Tue, 16 Jun 2020 09:34:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.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 09:34:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:57: 8000000 INFO @ Tue, 16 Jun 2020 09:35:03: 5000000 INFO @ Tue, 16 Jun 2020 09:35:05: 1000000 INFO @ Tue, 16 Jun 2020 09:35:05: 9000000 INFO @ Tue, 16 Jun 2020 09:35:10: 6000000 INFO @ Tue, 16 Jun 2020 09:35:13: 2000000 INFO @ Tue, 16 Jun 2020 09:35:13: 10000000 INFO @ Tue, 16 Jun 2020 09:35:18: 7000000 INFO @ Tue, 16 Jun 2020 09:35:21: 3000000 INFO @ Tue, 16 Jun 2020 09:35:21: 11000000 INFO @ Tue, 16 Jun 2020 09:35:25: 8000000 INFO @ Tue, 16 Jun 2020 09:35:29: 4000000 INFO @ Tue, 16 Jun 2020 09:35:29: 12000000 INFO @ Tue, 16 Jun 2020 09:35:32: 9000000 INFO @ Tue, 16 Jun 2020 09:35:37: 5000000 INFO @ Tue, 16 Jun 2020 09:35:37: 13000000 INFO @ Tue, 16 Jun 2020 09:35:40: 10000000 INFO @ Tue, 16 Jun 2020 09:35:45: 6000000 INFO @ Tue, 16 Jun 2020 09:35:45: 14000000 INFO @ Tue, 16 Jun 2020 09:35:47: 11000000 INFO @ Tue, 16 Jun 2020 09:35:53: 7000000 INFO @ Tue, 16 Jun 2020 09:35:53: 15000000 INFO @ Tue, 16 Jun 2020 09:35:54: 12000000 INFO @ Tue, 16 Jun 2020 09:36:01: 8000000 INFO @ Tue, 16 Jun 2020 09:36:02: 16000000 INFO @ Tue, 16 Jun 2020 09:36:02: 13000000 INFO @ Tue, 16 Jun 2020 09:36:09: 9000000 INFO @ Tue, 16 Jun 2020 09:36:10: 17000000 INFO @ Tue, 16 Jun 2020 09:36:10: 14000000 INFO @ Tue, 16 Jun 2020 09:36:16: 10000000 INFO @ Tue, 16 Jun 2020 09:36:17: 15000000 INFO @ Tue, 16 Jun 2020 09:36:17: 18000000 INFO @ Tue, 16 Jun 2020 09:36:24: 11000000 INFO @ Tue, 16 Jun 2020 09:36:25: 16000000 INFO @ Tue, 16 Jun 2020 09:36:25: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:32: 17000000 INFO @ Tue, 16 Jun 2020 09:36:32: 12000000 INFO @ Tue, 16 Jun 2020 09:36:33: 20000000 INFO @ Tue, 16 Jun 2020 09:36:39: 18000000 INFO @ Tue, 16 Jun 2020 09:36:40: 13000000 INFO @ Tue, 16 Jun 2020 09:36:41: 21000000 INFO @ Tue, 16 Jun 2020 09:36:47: 19000000 INFO @ Tue, 16 Jun 2020 09:36:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:36:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:36:48: #1 total tags in treatment: 21797631 INFO @ Tue, 16 Jun 2020 09:36:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:48: #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 09:36:48: 14000000 INFO @ Tue, 16 Jun 2020 09:36:48: #1 tags after filtering in treatment: 21797631 INFO @ Tue, 16 Jun 2020 09:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:50: #2 number of paired peaks: 1465 INFO @ Tue, 16 Jun 2020 09:36:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:50: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 09:36:50: #2 alternative fragment length(s) may be 2,133,148 bps INFO @ Tue, 16 Jun 2020 09:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.05_model.r INFO @ Tue, 16 Jun 2020 09:36:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:54: 20000000 INFO @ Tue, 16 Jun 2020 09:36:56: 15000000 INFO @ Tue, 16 Jun 2020 09:37:01: 21000000 INFO @ Tue, 16 Jun 2020 09:37:04: 16000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:37:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:37:07: #1 total tags in treatment: 21797631 INFO @ Tue, 16 Jun 2020 09:37:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:07: #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 09:37:08: #1 tags after filtering in treatment: 21797631 INFO @ Tue, 16 Jun 2020 09:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:09: #2 number of paired peaks: 1465 INFO @ Tue, 16 Jun 2020 09:37:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:10: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 09:37:10: #2 alternative fragment length(s) may be 2,133,148 bps INFO @ Tue, 16 Jun 2020 09:37:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.10_model.r INFO @ Tue, 16 Jun 2020 09:37:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:12: 17000000 INFO @ Tue, 16 Jun 2020 09:37:19: 18000000 INFO @ Tue, 16 Jun 2020 09:37:26: 19000000 INFO @ Tue, 16 Jun 2020 09:37:33: 20000000 INFO @ Tue, 16 Jun 2020 09:37:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:40: 21000000 INFO @ Tue, 16 Jun 2020 09:37:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:37:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:37:46: #1 total tags in treatment: 21797631 INFO @ Tue, 16 Jun 2020 09:37:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:46: #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 09:37:47: #1 tags after filtering in treatment: 21797631 INFO @ Tue, 16 Jun 2020 09:37:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:48: #2 number of paired peaks: 1465 INFO @ Tue, 16 Jun 2020 09:37:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:48: #2 predicted fragment length is 133 bps INFO @ Tue, 16 Jun 2020 09:37:48: #2 alternative fragment length(s) may be 2,133,148 bps INFO @ Tue, 16 Jun 2020 09:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.20_model.r INFO @ Tue, 16 Jun 2020 09:37:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.05_summits.bed INFO @ Tue, 16 Jun 2020 09:38:00: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6455 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.10_summits.bed INFO @ Tue, 16 Jun 2020 09:38:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3645 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494920/SRX494920.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1401 records, 4 fields): 3 millis CompletedMACS2peakCalling