Job ID = 6368162 SRX = SRX494846 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:55:18 prefetch.2.10.7: 1) Downloading 'SRR1198378'... 2020-06-15T23:55:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:57:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:57:15 prefetch.2.10.7: 1) 'SRR1198378' was downloaded successfully Read 12714648 spots for SRR1198378/SRR1198378.sra Written 12714648 spots for SRR1198378/SRR1198378.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: 00:02:27 12714648 reads; of these: 12714648 (100.00%) were unpaired; of these: 113187 (0.89%) aligned 0 times 10955728 (86.17%) aligned exactly 1 time 1645733 (12.94%) aligned >1 times 99.11% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 1313692 / 12601461 = 0.1042 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 09:03:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.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 09:03:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:03:36: 1000000 INFO @ Tue, 16 Jun 2020 09:03:41: 2000000 INFO @ Tue, 16 Jun 2020 09:03:46: 3000000 INFO @ Tue, 16 Jun 2020 09:03:51: 4000000 INFO @ Tue, 16 Jun 2020 09:03:56: 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 @ Tue, 16 Jun 2020 09:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.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 09:04:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:01: 6000000 INFO @ Tue, 16 Jun 2020 09:04:06: 1000000 INFO @ Tue, 16 Jun 2020 09:04:06: 7000000 INFO @ Tue, 16 Jun 2020 09:04:11: 2000000 INFO @ Tue, 16 Jun 2020 09:04:12: 8000000 INFO @ Tue, 16 Jun 2020 09:04:17: 3000000 INFO @ Tue, 16 Jun 2020 09:04:17: 9000000 INFO @ Tue, 16 Jun 2020 09:04:22: 10000000 INFO @ Tue, 16 Jun 2020 09:04:23: 4000000 INFO @ Tue, 16 Jun 2020 09:04:28: 11000000 INFO @ Tue, 16 Jun 2020 09:04:28: 5000000 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 09:04:29: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:04:29: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:04:29: #1 total tags in treatment: 11287769 INFO @ Tue, 16 Jun 2020 09:04:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:04:29: #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 09:04:30: #1 tags after filtering in treatment: 11287769 INFO @ Tue, 16 Jun 2020 09:04:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:04:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:04:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:04:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:04:30: #2 number of paired peaks: 105 WARNING @ Tue, 16 Jun 2020 09:04:30: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 16 Jun 2020 09:04:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:04:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:04:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:04:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:04:30: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:04:30: #2 alternative fragment length(s) may be 2,42,90,590 bps INFO @ Tue, 16 Jun 2020 09:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.05_model.r WARNING @ Tue, 16 Jun 2020 09:04:30: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:04:30: #2 You may need to consider one of the other alternative d(s): 2,42,90,590 WARNING @ Tue, 16 Jun 2020 09:04:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:04:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:04:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.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 09:04:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:34: 6000000 INFO @ Tue, 16 Jun 2020 09:04:37: 1000000 INFO @ Tue, 16 Jun 2020 09:04:40: 7000000 INFO @ Tue, 16 Jun 2020 09:04:44: 2000000 INFO @ Tue, 16 Jun 2020 09:04:45: 8000000 INFO @ Tue, 16 Jun 2020 09:04:50: 3000000 INFO @ Tue, 16 Jun 2020 09:04:51: 9000000 INFO @ Tue, 16 Jun 2020 09:04:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:57: 4000000 INFO @ Tue, 16 Jun 2020 09:04:57: 10000000 INFO @ Tue, 16 Jun 2020 09:05:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.05_summits.bed INFO @ Tue, 16 Jun 2020 09:05:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (581 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:05:03: 5000000 INFO @ Tue, 16 Jun 2020 09:05:03: 11000000 INFO @ Tue, 16 Jun 2020 09:05:05: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:05:05: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:05:05: #1 total tags in treatment: 11287769 INFO @ Tue, 16 Jun 2020 09:05:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:05: #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 09:05:05: #1 tags after filtering in treatment: 11287769 INFO @ Tue, 16 Jun 2020 09:05:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:06: #2 number of paired peaks: 105 WARNING @ Tue, 16 Jun 2020 09:05:06: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:06: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:05:06: #2 alternative fragment length(s) may be 2,42,90,590 bps INFO @ Tue, 16 Jun 2020 09:05:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.10_model.r WARNING @ Tue, 16 Jun 2020 09:05:06: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:06: #2 You may need to consider one of the other alternative d(s): 2,42,90,590 WARNING @ Tue, 16 Jun 2020 09:05:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:05:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:09: 6000000 INFO @ Tue, 16 Jun 2020 09:05:15: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:05:21: 8000000 INFO @ Tue, 16 Jun 2020 09:05:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:05:27: 9000000 INFO @ Tue, 16 Jun 2020 09:05:33: 10000000 INFO @ Tue, 16 Jun 2020 09:05:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.10_summits.bed INFO @ Tue, 16 Jun 2020 09:05:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:05:39: 11000000 INFO @ Tue, 16 Jun 2020 09:05:41: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:05:41: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:05:41: #1 total tags in treatment: 11287769 INFO @ Tue, 16 Jun 2020 09:05:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:41: #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 09:05:41: #1 tags after filtering in treatment: 11287769 INFO @ Tue, 16 Jun 2020 09:05:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:42: #2 number of paired peaks: 105 WARNING @ Tue, 16 Jun 2020 09:05:42: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:42: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:05:42: #2 alternative fragment length(s) may be 2,42,90,590 bps INFO @ Tue, 16 Jun 2020 09:05:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.20_model.r WARNING @ Tue, 16 Jun 2020 09:05:42: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:42: #2 You may need to consider one of the other alternative d(s): 2,42,90,590 WARNING @ Tue, 16 Jun 2020 09:05:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:05:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:06:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494846/SRX494846.20_summits.bed INFO @ Tue, 16 Jun 2020 09:06:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 1 millis CompletedMACS2peakCalling