Job ID = 6368972 SRX = SRX7971797 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:32:46 prefetch.2.10.7: 1) Downloading 'SRR11392683'... 2020-06-16T00:32:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:26 prefetch.2.10.7: 1) 'SRR11392683' was downloaded successfully 2020-06-16T00:35:26 prefetch.2.10.7: 'SRR11392683' has 0 unresolved dependencies Read 23425507 spots for SRR11392683/SRR11392683.sra Written 23425507 spots for SRR11392683/SRR11392683.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: 00:07:09 23425507 reads; of these: 23425507 (100.00%) were unpaired; of these: 218677 (0.93%) aligned 0 times 20912239 (89.27%) aligned exactly 1 time 2294591 (9.80%) aligned >1 times 99.07% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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_rmdupse_core] 5066027 / 23206830 = 0.2183 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 09:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.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 09:49:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:37: 1000000 INFO @ Tue, 16 Jun 2020 09:49:43: 2000000 INFO @ Tue, 16 Jun 2020 09:49:48: 3000000 INFO @ Tue, 16 Jun 2020 09:49:54: 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 @ Tue, 16 Jun 2020 09:50:00: 5000000 INFO @ Tue, 16 Jun 2020 09:50:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.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 09:50:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:06: 6000000 INFO @ Tue, 16 Jun 2020 09:50:08: 1000000 INFO @ Tue, 16 Jun 2020 09:50:12: 7000000 INFO @ Tue, 16 Jun 2020 09:50:14: 2000000 INFO @ Tue, 16 Jun 2020 09:50:19: 8000000 INFO @ Tue, 16 Jun 2020 09:50:21: 3000000 INFO @ Tue, 16 Jun 2020 09:50:25: 9000000 INFO @ Tue, 16 Jun 2020 09:50:28: 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 @ Tue, 16 Jun 2020 09:50:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.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 09:50:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:31: 10000000 INFO @ Tue, 16 Jun 2020 09:50:34: 5000000 INFO @ Tue, 16 Jun 2020 09:50:38: 11000000 INFO @ Tue, 16 Jun 2020 09:50:40: 1000000 INFO @ Tue, 16 Jun 2020 09:50:42: 6000000 INFO @ Tue, 16 Jun 2020 09:50:45: 12000000 INFO @ Tue, 16 Jun 2020 09:50:48: 2000000 INFO @ Tue, 16 Jun 2020 09:50:49: 7000000 INFO @ Tue, 16 Jun 2020 09:50:52: 13000000 INFO @ Tue, 16 Jun 2020 09:50:56: 3000000 INFO @ Tue, 16 Jun 2020 09:50:56: 8000000 INFO @ Tue, 16 Jun 2020 09:50:59: 14000000 INFO @ Tue, 16 Jun 2020 09:51:03: 9000000 INFO @ Tue, 16 Jun 2020 09:51:04: 4000000 INFO @ Tue, 16 Jun 2020 09:51:06: 15000000 INFO @ Tue, 16 Jun 2020 09:51:10: 10000000 INFO @ Tue, 16 Jun 2020 09:51:12: 16000000 INFO @ Tue, 16 Jun 2020 09:51:13: 5000000 INFO @ Tue, 16 Jun 2020 09:51:17: 11000000 INFO @ Tue, 16 Jun 2020 09:51:19: 17000000 INFO @ Tue, 16 Jun 2020 09:51:21: 6000000 INFO @ Tue, 16 Jun 2020 09:51:24: 12000000 INFO @ Tue, 16 Jun 2020 09:51:26: 18000000 INFO @ Tue, 16 Jun 2020 09:51:27: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:27: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:27: #1 total tags in treatment: 18140803 INFO @ Tue, 16 Jun 2020 09:51:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:27: #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 09:51:28: #1 tags after filtering in treatment: 18140803 INFO @ Tue, 16 Jun 2020 09:51:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:29: 7000000 INFO @ Tue, 16 Jun 2020 09:51:29: #2 number of paired peaks: 2417 INFO @ Tue, 16 Jun 2020 09:51:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:29: #2 predicted fragment length is 240 bps INFO @ Tue, 16 Jun 2020 09:51:29: #2 alternative fragment length(s) may be 4,240 bps INFO @ Tue, 16 Jun 2020 09:51:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.05_model.r INFO @ Tue, 16 Jun 2020 09:51:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:31: 13000000 INFO @ Tue, 16 Jun 2020 09:51:36: 8000000 INFO @ Tue, 16 Jun 2020 09:51:38: 14000000 INFO @ Tue, 16 Jun 2020 09:51:44: 9000000 INFO @ Tue, 16 Jun 2020 09:51:44: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:51:51: 16000000 INFO @ Tue, 16 Jun 2020 09:51:51: 10000000 INFO @ Tue, 16 Jun 2020 09:51:58: 17000000 INFO @ Tue, 16 Jun 2020 09:51:59: 11000000 INFO @ Tue, 16 Jun 2020 09:52:04: 18000000 INFO @ Tue, 16 Jun 2020 09:52:05: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:52:05: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:52:05: #1 total tags in treatment: 18140803 INFO @ Tue, 16 Jun 2020 09:52:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:05: #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 09:52:06: #1 tags after filtering in treatment: 18140803 INFO @ Tue, 16 Jun 2020 09:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:06: 12000000 INFO @ Tue, 16 Jun 2020 09:52:07: #2 number of paired peaks: 2417 INFO @ Tue, 16 Jun 2020 09:52:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:07: #2 predicted fragment length is 240 bps INFO @ Tue, 16 Jun 2020 09:52:07: #2 alternative fragment length(s) may be 4,240 bps INFO @ Tue, 16 Jun 2020 09:52:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.10_model.r INFO @ Tue, 16 Jun 2020 09:52:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:13: 13000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:52:20: 14000000 INFO @ Tue, 16 Jun 2020 09:52:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:27: 15000000 INFO @ Tue, 16 Jun 2020 09:52:34: 16000000 INFO @ Tue, 16 Jun 2020 09:52:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:41: 17000000 INFO @ Tue, 16 Jun 2020 09:52:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:41: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10904 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:48: 18000000 INFO @ Tue, 16 Jun 2020 09:52:49: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:52:49: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:52:49: #1 total tags in treatment: 18140803 INFO @ Tue, 16 Jun 2020 09:52:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:49: #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 09:52:50: #1 tags after filtering in treatment: 18140803 INFO @ Tue, 16 Jun 2020 09:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:51: #2 number of paired peaks: 2417 INFO @ Tue, 16 Jun 2020 09:52:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:51: #2 predicted fragment length is 240 bps INFO @ Tue, 16 Jun 2020 09:52:51: #2 alternative fragment length(s) may be 4,240 bps INFO @ Tue, 16 Jun 2020 09:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.20_model.r INFO @ Tue, 16 Jun 2020 09:52:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:18: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7755 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971797/SRX7971797.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3985 records, 4 fields): 5 millis CompletedMACS2peakCalling