Job ID = 5720243 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,745,046 reads read : 10,745,046 reads written : 10,745,046 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:02:24 10745046 reads; of these: 10745046 (100.00%) were unpaired; of these: 569015 (5.30%) aligned 0 times 8769803 (81.62%) aligned exactly 1 time 1406228 (13.09%) aligned >1 times 94.70% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 1562086 / 10176031 = 0.1535 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 @ Wed, 15 Apr 2020 22:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.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 @ Wed, 15 Apr 2020 22:45:53: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:45:53: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:45:58: 1000000 INFO @ Wed, 15 Apr 2020 22:46:03: 2000000 INFO @ Wed, 15 Apr 2020 22:46:08: 3000000 INFO @ Wed, 15 Apr 2020 22:46:14: 4000000 INFO @ Wed, 15 Apr 2020 22:46:19: 5000000 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 @ Wed, 15 Apr 2020 22:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.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 @ Wed, 15 Apr 2020 22:46:23: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:46:23: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:46:24: 6000000 INFO @ Wed, 15 Apr 2020 22:46:28: 1000000 INFO @ Wed, 15 Apr 2020 22:46:30: 7000000 INFO @ Wed, 15 Apr 2020 22:46:34: 2000000 INFO @ Wed, 15 Apr 2020 22:46:36: 8000000 INFO @ Wed, 15 Apr 2020 22:46:39: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:46:39: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:46:39: #1 total tags in treatment: 8613945 INFO @ Wed, 15 Apr 2020 22:46:39: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:46:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:46:39: #1 tags after filtering in treatment: 8613945 INFO @ Wed, 15 Apr 2020 22:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:46:39: #1 finished! INFO @ Wed, 15 Apr 2020 22:46:39: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:46:40: 3000000 INFO @ Wed, 15 Apr 2020 22:46:40: #2 number of paired peaks: 656 WARNING @ Wed, 15 Apr 2020 22:46:40: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Wed, 15 Apr 2020 22:46:40: start model_add_line... INFO @ Wed, 15 Apr 2020 22:46:40: start X-correlation... INFO @ Wed, 15 Apr 2020 22:46:40: end of X-cor INFO @ Wed, 15 Apr 2020 22:46:40: #2 finished! INFO @ Wed, 15 Apr 2020 22:46:40: #2 predicted fragment length is 131 bps INFO @ Wed, 15 Apr 2020 22:46:40: #2 alternative fragment length(s) may be 131 bps INFO @ Wed, 15 Apr 2020 22:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.05_model.r INFO @ Wed, 15 Apr 2020 22:46:40: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:46:45: 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 @ Wed, 15 Apr 2020 22:46:50: 5000000 INFO @ Wed, 15 Apr 2020 22:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.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 @ Wed, 15 Apr 2020 22:46:53: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:46:53: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:46:56: 6000000 INFO @ Wed, 15 Apr 2020 22:46:58: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:46:59: 1000000 INFO @ Wed, 15 Apr 2020 22:47:02: 7000000 INFO @ Wed, 15 Apr 2020 22:47:04: 2000000 INFO @ Wed, 15 Apr 2020 22:47:07: 8000000 INFO @ Wed, 15 Apr 2020 22:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.05_summits.bed INFO @ Wed, 15 Apr 2020 22:47:08: Done! INFO @ Wed, 15 Apr 2020 22:47:10: 3000000 INFO @ Wed, 15 Apr 2020 22:47:11: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:47:11: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:47:11: #1 total tags in treatment: 8613945 INFO @ Wed, 15 Apr 2020 22:47:11: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:47:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:47:11: #1 tags after filtering in treatment: 8613945 INFO @ Wed, 15 Apr 2020 22:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:47:11: #1 finished! INFO @ Wed, 15 Apr 2020 22:47:11: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:47:11: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3813 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:47:11: #2 number of paired peaks: 656 WARNING @ Wed, 15 Apr 2020 22:47:11: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Wed, 15 Apr 2020 22:47:11: start model_add_line... INFO @ Wed, 15 Apr 2020 22:47:11: start X-correlation... INFO @ Wed, 15 Apr 2020 22:47:11: end of X-cor INFO @ Wed, 15 Apr 2020 22:47:11: #2 finished! INFO @ Wed, 15 Apr 2020 22:47:11: #2 predicted fragment length is 131 bps INFO @ Wed, 15 Apr 2020 22:47:11: #2 alternative fragment length(s) may be 131 bps INFO @ Wed, 15 Apr 2020 22:47:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.10_model.r INFO @ Wed, 15 Apr 2020 22:47:11: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:47:15: 4000000 INFO @ Wed, 15 Apr 2020 22:47:21: 5000000 INFO @ Wed, 15 Apr 2020 22:47:26: 6000000 INFO @ Wed, 15 Apr 2020 22:47:30: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:47:31: 7000000 INFO @ Wed, 15 Apr 2020 22:47:36: 8000000 INFO @ Wed, 15 Apr 2020 22:47:39: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:47:39: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:47:39: #1 total tags in treatment: 8613945 INFO @ Wed, 15 Apr 2020 22:47:39: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:47:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:47:39: #1 tags after filtering in treatment: 8613945 INFO @ Wed, 15 Apr 2020 22:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:47:39: #1 finished! INFO @ Wed, 15 Apr 2020 22:47:39: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.10_summits.bed INFO @ Wed, 15 Apr 2020 22:47:40: Done! INFO @ Wed, 15 Apr 2020 22:47:40: #2 number of paired peaks: 656 WARNING @ Wed, 15 Apr 2020 22:47:40: Fewer paired peaks (656) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 656 pairs to build model! INFO @ Wed, 15 Apr 2020 22:47:40: start model_add_line... INFO @ Wed, 15 Apr 2020 22:47:40: start X-correlation... INFO @ Wed, 15 Apr 2020 22:47:40: end of X-cor INFO @ Wed, 15 Apr 2020 22:47:40: #2 finished! INFO @ Wed, 15 Apr 2020 22:47:40: #2 predicted fragment length is 131 bps INFO @ Wed, 15 Apr 2020 22:47:40: #2 alternative fragment length(s) may be 131 bps INFO @ Wed, 15 Apr 2020 22:47:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.20_model.r INFO @ Wed, 15 Apr 2020 22:47:40: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:47:40: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1722 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:47:57: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720188/SRX6720188.20_summits.bed INFO @ Wed, 15 Apr 2020 22:48:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。