Job ID = 6365929 SRX = SRX043862 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:14:57 prefetch.2.10.7: 1) Downloading 'SRR107322'... 2020-06-15T22:14:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:15:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:15:37 prefetch.2.10.7: 'SRR107322' is valid 2020-06-15T22:15:37 prefetch.2.10.7: 1) 'SRR107322' was downloaded successfully Read 6191439 spots for SRR107322/SRR107322.sra Written 6191439 spots for SRR107322/SRR107322.sra 2020-06-15T22:16:04 prefetch.2.10.7: 1) Downloading 'SRR107323'... 2020-06-15T22:16:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:16:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:16:36 prefetch.2.10.7: 'SRR107323' is valid 2020-06-15T22:16:36 prefetch.2.10.7: 1) 'SRR107323' was downloaded successfully Read 5071217 spots for SRR107323/SRR107323.sra Written 5071217 spots for SRR107323/SRR107323.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: 00:00:59 11262656 reads; of these: 11262656 (100.00%) were unpaired; of these: 9329532 (82.84%) aligned 0 times 1695622 (15.06%) aligned exactly 1 time 237502 (2.11%) aligned >1 times 17.16% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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_rmdupse_core] 173816 / 1933124 = 0.0899 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 07:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.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 07:18:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:18:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:18:58: 1000000 INFO @ Tue, 16 Jun 2020 07:19:02: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:19:02: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:19:02: #1 total tags in treatment: 1759308 INFO @ Tue, 16 Jun 2020 07:19:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:19:02: #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 07:19:02: #1 tags after filtering in treatment: 1759308 INFO @ Tue, 16 Jun 2020 07:19:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:19:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:19:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:19:02: #2 number of paired peaks: 583 WARNING @ Tue, 16 Jun 2020 07:19:02: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Tue, 16 Jun 2020 07:19:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:19:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:19:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:19:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:19:02: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 07:19:02: #2 alternative fragment length(s) may be 146,582 bps INFO @ Tue, 16 Jun 2020 07:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.05_model.r INFO @ Tue, 16 Jun 2020 07:19:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:19:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:19:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:19:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:19:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.05_summits.bed INFO @ Tue, 16 Jun 2020 07:19:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1212 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 07:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.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 07:19:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:19:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:19:27: 1000000 INFO @ Tue, 16 Jun 2020 07:19:30: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:19:30: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:19:30: #1 total tags in treatment: 1759308 INFO @ Tue, 16 Jun 2020 07:19:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:19:30: #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 07:19:30: #1 tags after filtering in treatment: 1759308 INFO @ Tue, 16 Jun 2020 07:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:19:30: #1 finished! INFO @ Tue, 16 Jun 2020 07:19:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:19:30: #2 number of paired peaks: 583 WARNING @ Tue, 16 Jun 2020 07:19:30: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Tue, 16 Jun 2020 07:19:30: start model_add_line... INFO @ Tue, 16 Jun 2020 07:19:30: start X-correlation... INFO @ Tue, 16 Jun 2020 07:19:30: end of X-cor INFO @ Tue, 16 Jun 2020 07:19:30: #2 finished! INFO @ Tue, 16 Jun 2020 07:19:30: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 07:19:30: #2 alternative fragment length(s) may be 146,582 bps INFO @ Tue, 16 Jun 2020 07:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.10_model.r INFO @ Tue, 16 Jun 2020 07:19:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:19:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:19:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:19:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:19:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.10_summits.bed INFO @ Tue, 16 Jun 2020 07:19:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (396 records, 4 fields): 2 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 07:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.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 07:19:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:19:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:19:56: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:20:00: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:20:00: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:20:00: #1 total tags in treatment: 1759308 INFO @ Tue, 16 Jun 2020 07:20:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:20:00: #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 07:20:00: #1 tags after filtering in treatment: 1759308 INFO @ Tue, 16 Jun 2020 07:20:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:20:00: #1 finished! INFO @ Tue, 16 Jun 2020 07:20:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:20:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:20:00: #2 number of paired peaks: 583 WARNING @ Tue, 16 Jun 2020 07:20:00: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Tue, 16 Jun 2020 07:20:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:20:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:20:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:20:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:20:00: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 07:20:00: #2 alternative fragment length(s) may be 146,582 bps INFO @ Tue, 16 Jun 2020 07:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.20_model.r INFO @ Tue, 16 Jun 2020 07:20:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:20:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:20:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:20:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:20:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:20:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043862/SRX043862.20_summits.bed INFO @ Tue, 16 Jun 2020 07:20:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (71 records, 4 fields): 1 millis CompletedMACS2peakCalling