Job ID = 6366934 SRX = SRX2576636 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:08 prefetch.2.10.7: 1) Downloading 'SRR5272593'... 2020-06-15T23:06:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:17 prefetch.2.10.7: 'SRR5272593' is valid 2020-06-15T23:07:17 prefetch.2.10.7: 1) 'SRR5272593' was downloaded successfully Read 19947557 spots for SRR5272593/SRR5272593.sra Written 19947557 spots for SRR5272593/SRR5272593.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: 00:02:53 19947557 reads; of these: 19947557 (100.00%) were unpaired; of these: 715513 (3.59%) aligned 0 times 15851313 (79.46%) aligned exactly 1 time 3380731 (16.95%) aligned >1 times 96.41% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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 8 files... [bam_rmdupse_core] 3301804 / 19232044 = 0.1717 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 08:16:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.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 08:16:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:40: 1000000 INFO @ Tue, 16 Jun 2020 08:16:46: 2000000 INFO @ Tue, 16 Jun 2020 08:16:52: 3000000 INFO @ Tue, 16 Jun 2020 08:16:57: 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 08:17:03: 5000000 INFO @ Tue, 16 Jun 2020 08:17:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.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 08:17:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:08: 6000000 INFO @ Tue, 16 Jun 2020 08:17:10: 1000000 INFO @ Tue, 16 Jun 2020 08:17:14: 7000000 INFO @ Tue, 16 Jun 2020 08:17:16: 2000000 INFO @ Tue, 16 Jun 2020 08:17:20: 8000000 INFO @ Tue, 16 Jun 2020 08:17:22: 3000000 INFO @ Tue, 16 Jun 2020 08:17:25: 9000000 INFO @ Tue, 16 Jun 2020 08:17:28: 4000000 INFO @ Tue, 16 Jun 2020 08:17:31: 10000000 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 08:17:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.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 08:17:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:34: 5000000 INFO @ Tue, 16 Jun 2020 08:17:37: 11000000 INFO @ Tue, 16 Jun 2020 08:17:41: 1000000 INFO @ Tue, 16 Jun 2020 08:17:41: 6000000 INFO @ Tue, 16 Jun 2020 08:17:42: 12000000 INFO @ Tue, 16 Jun 2020 08:17:48: 2000000 INFO @ Tue, 16 Jun 2020 08:17:48: 13000000 INFO @ Tue, 16 Jun 2020 08:17:48: 7000000 INFO @ Tue, 16 Jun 2020 08:17:54: 14000000 INFO @ Tue, 16 Jun 2020 08:17:55: 3000000 INFO @ Tue, 16 Jun 2020 08:17:55: 8000000 INFO @ Tue, 16 Jun 2020 08:18:00: 15000000 INFO @ Tue, 16 Jun 2020 08:18:02: 4000000 INFO @ Tue, 16 Jun 2020 08:18:03: 9000000 INFO @ Tue, 16 Jun 2020 08:18:06: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:18:06: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:18:06: #1 total tags in treatment: 15930240 INFO @ Tue, 16 Jun 2020 08:18:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:06: #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 08:18:06: #1 tags after filtering in treatment: 15930240 INFO @ Tue, 16 Jun 2020 08:18:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:07: #2 number of paired peaks: 522 WARNING @ Tue, 16 Jun 2020 08:18:07: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:07: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 08:18:07: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 08:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.05_model.r INFO @ Tue, 16 Jun 2020 08:18:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:09: 5000000 INFO @ Tue, 16 Jun 2020 08:18:10: 10000000 INFO @ Tue, 16 Jun 2020 08:18:16: 6000000 INFO @ Tue, 16 Jun 2020 08:18:16: 11000000 INFO @ Tue, 16 Jun 2020 08:18:23: 7000000 INFO @ Tue, 16 Jun 2020 08:18:23: 12000000 INFO @ Tue, 16 Jun 2020 08:18:30: 8000000 INFO @ Tue, 16 Jun 2020 08:18:31: 13000000 INFO @ Tue, 16 Jun 2020 08:18:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:37: 9000000 INFO @ Tue, 16 Jun 2020 08:18:38: 14000000 INFO @ Tue, 16 Jun 2020 08:18:45: 10000000 INFO @ Tue, 16 Jun 2020 08:18:45: 15000000 INFO @ Tue, 16 Jun 2020 08:18:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2798 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:52: 11000000 INFO @ Tue, 16 Jun 2020 08:18:52: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:18:52: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:18:52: #1 total tags in treatment: 15930240 INFO @ Tue, 16 Jun 2020 08:18:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:52: #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 08:18:52: #1 tags after filtering in treatment: 15930240 INFO @ Tue, 16 Jun 2020 08:18:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:53: #2 number of paired peaks: 522 WARNING @ Tue, 16 Jun 2020 08:18:53: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:53: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 08:18:53: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 08:18:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.10_model.r INFO @ Tue, 16 Jun 2020 08:18:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:18:58: 12000000 INFO @ Tue, 16 Jun 2020 08:19:04: 13000000 INFO @ Tue, 16 Jun 2020 08:19:11: 14000000 INFO @ Tue, 16 Jun 2020 08:19:17: 15000000 INFO @ Tue, 16 Jun 2020 08:19:23: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:19:23: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:19:23: #1 total tags in treatment: 15930240 INFO @ Tue, 16 Jun 2020 08:19:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:23: #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 08:19:24: #1 tags after filtering in treatment: 15930240 INFO @ Tue, 16 Jun 2020 08:19:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:25: #2 number of paired peaks: 522 WARNING @ Tue, 16 Jun 2020 08:19:25: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:25: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 08:19:25: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 08:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.20_model.r INFO @ Tue, 16 Jun 2020 08:19:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.10_summits.bed INFO @ Tue, 16 Jun 2020 08:19:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1997 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:19:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576636/SRX2576636.20_summits.bed INFO @ Tue, 16 Jun 2020 08:20:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1367 records, 4 fields): 3 millis CompletedMACS2peakCalling