Job ID = 6368107 SRX = SRX466570 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:01:30 prefetch.2.10.7: 1) Downloading 'SRR1163636'... 2020-06-16T00:01:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:04:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:04:17 prefetch.2.10.7: 1) 'SRR1163636' was downloaded successfully Read 22919297 spots for SRR1163636/SRR1163636.sra Written 22919297 spots for SRR1163636/SRR1163636.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: 00:03:25 22919297 reads; of these: 22919297 (100.00%) were unpaired; of these: 10578078 (46.15%) aligned 0 times 10179214 (44.41%) aligned exactly 1 time 2162005 (9.43%) aligned >1 times 53.85% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 11437807 / 12341219 = 0.9268 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 09:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.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 09:11:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:58: #1 total tags in treatment: 903412 INFO @ Tue, 16 Jun 2020 09:11:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:58: #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 09:11:58: #1 tags after filtering in treatment: 903412 INFO @ Tue, 16 Jun 2020 09:11:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:59: #2 number of paired peaks: 1664 INFO @ Tue, 16 Jun 2020 09:11:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:59: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:11:59: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 16 Jun 2020 09:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:59: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:59: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 16 Jun 2020 09:11:59: #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 09:11:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (739 records, 4 fields): 2 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 09:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.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 09:12:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:27: #1 total tags in treatment: 903412 INFO @ Tue, 16 Jun 2020 09:12:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:27: #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 09:12:27: #1 tags after filtering in treatment: 903412 INFO @ Tue, 16 Jun 2020 09:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:27: #2 number of paired peaks: 1664 INFO @ Tue, 16 Jun 2020 09:12:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:27: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:12:27: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 16 Jun 2020 09:12:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:27: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:27: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 16 Jun 2020 09:12:27: #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 09:12:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 1 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 09:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.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 09:12:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:52: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:57: #1 total tags in treatment: 903412 INFO @ Tue, 16 Jun 2020 09:12:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:57: #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 09:12:57: #1 tags after filtering in treatment: 903412 INFO @ Tue, 16 Jun 2020 09:12:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:57: #2 number of paired peaks: 1664 INFO @ Tue, 16 Jun 2020 09:12:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:57: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:12:57: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 16 Jun 2020 09:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:58: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:58: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 16 Jun 2020 09:12:58: #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 09:12:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466570/SRX466570.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 1 millis CompletedMACS2peakCalling