Job ID = 6507821 SRX = SRX494826 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:52:35 prefetch.2.10.7: 1) Downloading 'SRR1198358'... 2020-06-26T12:52:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:53:37 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:53:37 prefetch.2.10.7: 'SRR1198358' is valid 2020-06-26T12:53:37 prefetch.2.10.7: 1) 'SRR1198358' was downloaded successfully Read 16052001 spots for SRR1198358/SRR1198358.sra Written 16052001 spots for SRR1198358/SRR1198358.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:06 16052001 reads; of these: 16052001 (100.00%) were unpaired; of these: 5228146 (32.57%) aligned 0 times 8839196 (55.07%) aligned exactly 1 time 1984659 (12.36%) aligned >1 times 67.43% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 1604456 / 10823855 = 0.1482 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 @ Fri, 26 Jun 2020 21:58:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.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 @ Fri, 26 Jun 2020 21:58:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:58:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:59:04: 1000000 INFO @ Fri, 26 Jun 2020 21:59:10: 2000000 INFO @ Fri, 26 Jun 2020 21:59:17: 3000000 INFO @ Fri, 26 Jun 2020 21:59:23: 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 @ Fri, 26 Jun 2020 21:59:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.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 @ Fri, 26 Jun 2020 21:59:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:59:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:59:29: 5000000 INFO @ Fri, 26 Jun 2020 21:59:35: 1000000 INFO @ Fri, 26 Jun 2020 21:59:36: 6000000 INFO @ Fri, 26 Jun 2020 21:59:42: 2000000 INFO @ Fri, 26 Jun 2020 21:59:42: 7000000 INFO @ Fri, 26 Jun 2020 21:59:49: 3000000 INFO @ Fri, 26 Jun 2020 21:59:49: 8000000 INFO @ Fri, 26 Jun 2020 21:59:56: 9000000 INFO @ Fri, 26 Jun 2020 21:59:56: 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 @ Fri, 26 Jun 2020 21:59:57: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 21:59:57: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 21:59:57: #1 total tags in treatment: 9219399 INFO @ Fri, 26 Jun 2020 21:59:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:59:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 21:59:57: #1 tags after filtering in treatment: 9219399 INFO @ Fri, 26 Jun 2020 21:59:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:59:57: #1 finished! INFO @ Fri, 26 Jun 2020 21:59:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:59:58: #2 number of paired peaks: 402 WARNING @ Fri, 26 Jun 2020 21:59:58: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Fri, 26 Jun 2020 21:59:58: start model_add_line... INFO @ Fri, 26 Jun 2020 21:59:58: start X-correlation... INFO @ Fri, 26 Jun 2020 21:59:58: end of X-cor INFO @ Fri, 26 Jun 2020 21:59:58: #2 finished! INFO @ Fri, 26 Jun 2020 21:59:58: #2 predicted fragment length is 39 bps INFO @ Fri, 26 Jun 2020 21:59:58: #2 alternative fragment length(s) may be 2,39,583 bps INFO @ Fri, 26 Jun 2020 21:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.05_model.r WARNING @ Fri, 26 Jun 2020 21:59:58: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 21:59:58: #2 You may need to consider one of the other alternative d(s): 2,39,583 WARNING @ Fri, 26 Jun 2020 21:59:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 21:59:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 21:59:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.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 @ Fri, 26 Jun 2020 21:59:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:59:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:00:02: 5000000 INFO @ Fri, 26 Jun 2020 22:00:04: 1000000 INFO @ Fri, 26 Jun 2020 22:00:09: 6000000 INFO @ Fri, 26 Jun 2020 22:00:11: 2000000 INFO @ Fri, 26 Jun 2020 22:00:16: 7000000 INFO @ Fri, 26 Jun 2020 22:00:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:00:17: 3000000 INFO @ Fri, 26 Jun 2020 22:00:23: 8000000 INFO @ Fri, 26 Jun 2020 22:00:24: 4000000 INFO @ Fri, 26 Jun 2020 22:00:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:00:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:00:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.05_summits.bed INFO @ Fri, 26 Jun 2020 22:00:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (951 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:00:30: 9000000 INFO @ Fri, 26 Jun 2020 22:00:30: 5000000 INFO @ Fri, 26 Jun 2020 22:00:31: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:00:31: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:00:31: #1 total tags in treatment: 9219399 INFO @ Fri, 26 Jun 2020 22:00:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:00:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:00:31: #1 tags after filtering in treatment: 9219399 INFO @ Fri, 26 Jun 2020 22:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:00:31: #1 finished! INFO @ Fri, 26 Jun 2020 22:00:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:00:32: #2 number of paired peaks: 402 WARNING @ Fri, 26 Jun 2020 22:00:32: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Fri, 26 Jun 2020 22:00:32: start model_add_line... INFO @ Fri, 26 Jun 2020 22:00:32: start X-correlation... INFO @ Fri, 26 Jun 2020 22:00:32: end of X-cor INFO @ Fri, 26 Jun 2020 22:00:32: #2 finished! INFO @ Fri, 26 Jun 2020 22:00:32: #2 predicted fragment length is 39 bps INFO @ Fri, 26 Jun 2020 22:00:32: #2 alternative fragment length(s) may be 2,39,583 bps INFO @ Fri, 26 Jun 2020 22:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.10_model.r WARNING @ Fri, 26 Jun 2020 22:00:32: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:00:32: #2 You may need to consider one of the other alternative d(s): 2,39,583 WARNING @ Fri, 26 Jun 2020 22:00:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:00:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:00:36: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:00:42: 7000000 INFO @ Fri, 26 Jun 2020 22:00:48: 8000000 INFO @ Fri, 26 Jun 2020 22:00:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:00:53: 9000000 INFO @ Fri, 26 Jun 2020 22:00:55: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:00:55: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:00:55: #1 total tags in treatment: 9219399 INFO @ Fri, 26 Jun 2020 22:00:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:00:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:00:55: #1 tags after filtering in treatment: 9219399 INFO @ Fri, 26 Jun 2020 22:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:00:55: #1 finished! INFO @ Fri, 26 Jun 2020 22:00:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:00:55: #2 number of paired peaks: 402 WARNING @ Fri, 26 Jun 2020 22:00:55: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Fri, 26 Jun 2020 22:00:55: start model_add_line... INFO @ Fri, 26 Jun 2020 22:00:55: start X-correlation... INFO @ Fri, 26 Jun 2020 22:00:55: end of X-cor INFO @ Fri, 26 Jun 2020 22:00:55: #2 finished! INFO @ Fri, 26 Jun 2020 22:00:55: #2 predicted fragment length is 39 bps INFO @ Fri, 26 Jun 2020 22:00:55: #2 alternative fragment length(s) may be 2,39,583 bps INFO @ Fri, 26 Jun 2020 22:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.20_model.r WARNING @ Fri, 26 Jun 2020 22:00:55: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:00:55: #2 You may need to consider one of the other alternative d(s): 2,39,583 WARNING @ Fri, 26 Jun 2020 22:00:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:00:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:00:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:01:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:01:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:01:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.10_summits.bed INFO @ Fri, 26 Jun 2020 22:01:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:01:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:01:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494826/SRX494826.20_summits.bed INFO @ Fri, 26 Jun 2020 22:01:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 2 millis CompletedMACS2peakCalling