Job ID = 6366511 SRX = SRX1674091 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:53 prefetch.2.10.7: 1) Downloading 'SRR3320137'... 2020-06-15T23:00:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:05 prefetch.2.10.7: 1) 'SRR3320137' was downloaded successfully Read 37051917 spots for SRR3320137/SRR3320137.sra Written 37051917 spots for SRR3320137/SRR3320137.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: 00:07:01 37051917 reads; of these: 37051917 (100.00%) were unpaired; of these: 8366258 (22.58%) aligned 0 times 23189486 (62.59%) aligned exactly 1 time 5496173 (14.83%) aligned >1 times 77.42% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:01 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] 23214229 / 28685659 = 0.8093 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 08:17:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.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 08:17:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:06: 1000000 INFO @ Tue, 16 Jun 2020 08:17:12: 2000000 INFO @ Tue, 16 Jun 2020 08:17:18: 3000000 INFO @ Tue, 16 Jun 2020 08:17:24: 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 08:17:29: 5000000 INFO @ Tue, 16 Jun 2020 08:17:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.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 08:17:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:17:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:17:32: #1 total tags in treatment: 5471430 INFO @ Tue, 16 Jun 2020 08:17:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:32: #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 08:17:32: #1 tags after filtering in treatment: 5471430 INFO @ Tue, 16 Jun 2020 08:17:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:33: #2 number of paired peaks: 2103 INFO @ Tue, 16 Jun 2020 08:17:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:33: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 08:17:33: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 08:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.05_model.r INFO @ Tue, 16 Jun 2020 08:17:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:38: 1000000 INFO @ Tue, 16 Jun 2020 08:17:45: 2000000 INFO @ Tue, 16 Jun 2020 08:17:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:52: 3000000 INFO @ Tue, 16 Jun 2020 08:17:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.05_summits.bed INFO @ Tue, 16 Jun 2020 08:17:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7275 records, 4 fields): 8 millis CompletedMACS2peakCalling 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 08:17:59: 4000000 INFO @ Tue, 16 Jun 2020 08:18:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.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 08:18:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:07: 5000000 INFO @ Tue, 16 Jun 2020 08:18:08: 1000000 INFO @ Tue, 16 Jun 2020 08:18:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:18:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:18:11: #1 total tags in treatment: 5471430 INFO @ Tue, 16 Jun 2020 08:18:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:11: #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 08:18:11: #1 tags after filtering in treatment: 5471430 INFO @ Tue, 16 Jun 2020 08:18:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:12: #2 number of paired peaks: 2103 INFO @ Tue, 16 Jun 2020 08:18:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:12: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 08:18:12: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 08:18:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.10_model.r INFO @ Tue, 16 Jun 2020 08:18:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:15: 2000000 INFO @ Tue, 16 Jun 2020 08:18:22: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:18:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:29: 4000000 INFO @ Tue, 16 Jun 2020 08:18:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3445 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:36: 5000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:18:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:18:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:18:39: #1 total tags in treatment: 5471430 INFO @ Tue, 16 Jun 2020 08:18:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:39: #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 08:18:39: #1 tags after filtering in treatment: 5471430 INFO @ Tue, 16 Jun 2020 08:18:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:39: #2 number of paired peaks: 2103 INFO @ Tue, 16 Jun 2020 08:18:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:39: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 08:18:39: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 16 Jun 2020 08:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.20_model.r INFO @ Tue, 16 Jun 2020 08:18:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674091/SRX1674091.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1456 records, 4 fields): 3 millis CompletedMACS2peakCalling