Job ID = 6368196 SRX = SRX494880 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:58:20 prefetch.2.10.7: 1) Downloading 'SRR1198412'... 2020-06-15T23:58:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:35 prefetch.2.10.7: 1) 'SRR1198412' was downloaded successfully Read 22666423 spots for SRR1198412/SRR1198412.sra Written 22666423 spots for SRR1198412/SRR1198412.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: 00:05:19 22666423 reads; of these: 22666423 (100.00%) were unpaired; of these: 1047291 (4.62%) aligned 0 times 18456723 (81.43%) aligned exactly 1 time 3162409 (13.95%) aligned >1 times 95.38% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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 12 files... [bam_rmdupse_core] 12022536 / 21619132 = 0.5561 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 09:11:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.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 09:11:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:59: 1000000 INFO @ Tue, 16 Jun 2020 09:12:07: 2000000 INFO @ Tue, 16 Jun 2020 09:12:15: 3000000 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 09:12:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.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 09:12:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:23: 4000000 INFO @ Tue, 16 Jun 2020 09:12:30: 1000000 INFO @ Tue, 16 Jun 2020 09:12:32: 5000000 INFO @ Tue, 16 Jun 2020 09:12:40: 2000000 INFO @ Tue, 16 Jun 2020 09:12:41: 6000000 INFO @ Tue, 16 Jun 2020 09:12:49: 3000000 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 09:12:50: 7000000 INFO @ Tue, 16 Jun 2020 09:12:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.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 09:12:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:58: 4000000 INFO @ Tue, 16 Jun 2020 09:12:59: 8000000 INFO @ Tue, 16 Jun 2020 09:13:01: 1000000 INFO @ Tue, 16 Jun 2020 09:13:07: 5000000 INFO @ Tue, 16 Jun 2020 09:13:07: 9000000 INFO @ Tue, 16 Jun 2020 09:13:10: 2000000 INFO @ Tue, 16 Jun 2020 09:13:12: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:13:12: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:13:12: #1 total tags in treatment: 9596596 INFO @ Tue, 16 Jun 2020 09:13:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:12: #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 09:13:13: #1 tags after filtering in treatment: 9596596 INFO @ Tue, 16 Jun 2020 09:13:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:13: #2 number of paired peaks: 701 WARNING @ Tue, 16 Jun 2020 09:13:13: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:14: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 09:13:14: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 16 Jun 2020 09:13:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.05_model.r WARNING @ Tue, 16 Jun 2020 09:13:14: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:14: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 16 Jun 2020 09:13:14: #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 09:13:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:16: 6000000 INFO @ Tue, 16 Jun 2020 09:13:18: 3000000 INFO @ Tue, 16 Jun 2020 09:13:25: 7000000 INFO @ Tue, 16 Jun 2020 09:13:27: 4000000 INFO @ Tue, 16 Jun 2020 09:13:33: 8000000 INFO @ Tue, 16 Jun 2020 09:13:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:36: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:42: 9000000 INFO @ Tue, 16 Jun 2020 09:13:45: 6000000 INFO @ Tue, 16 Jun 2020 09:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.05_summits.bed INFO @ Tue, 16 Jun 2020 09:13:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2239 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:13:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:13:46: #1 total tags in treatment: 9596596 INFO @ Tue, 16 Jun 2020 09:13:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:46: #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 09:13:47: #1 tags after filtering in treatment: 9596596 INFO @ Tue, 16 Jun 2020 09:13:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:47: #2 number of paired peaks: 701 WARNING @ Tue, 16 Jun 2020 09:13:47: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:47: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 09:13:47: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 16 Jun 2020 09:13:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.10_model.r WARNING @ Tue, 16 Jun 2020 09:13:47: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:47: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 16 Jun 2020 09:13:47: #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 09:13:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:53: 7000000 INFO @ Tue, 16 Jun 2020 09:14:01: 8000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:14:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:09: 9000000 INFO @ Tue, 16 Jun 2020 09:14:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:14:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:14:13: #1 total tags in treatment: 9596596 INFO @ Tue, 16 Jun 2020 09:14:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:13: #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 09:14:14: #1 tags after filtering in treatment: 9596596 INFO @ Tue, 16 Jun 2020 09:14:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:14: #2 number of paired peaks: 701 WARNING @ Tue, 16 Jun 2020 09:14:14: Fewer paired peaks (701) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 701 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:14: #2 predicted fragment length is 61 bps INFO @ Tue, 16 Jun 2020 09:14:14: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 16 Jun 2020 09:14:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.20_model.r WARNING @ Tue, 16 Jun 2020 09:14:14: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:14:14: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 16 Jun 2020 09:14:14: #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 09:14:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.10_summits.bed INFO @ Tue, 16 Jun 2020 09:14:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (895 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494880/SRX494880.20_summits.bed INFO @ Tue, 16 Jun 2020 09:14:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 1 millis CompletedMACS2peakCalling