Job ID = 6368965 SRX = SRX7971791 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:34:51 prefetch.2.10.7: 1) Downloading 'SRR11392677'... 2020-06-16T00:34:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:39 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:39 prefetch.2.10.7: 1) 'SRR11392677' was downloaded successfully 2020-06-16T00:36:39 prefetch.2.10.7: 'SRR11392677' has 0 unresolved dependencies Read 26952738 spots for SRR11392677/SRR11392677.sra Written 26952738 spots for SRR11392677/SRR11392677.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: 00:11:44 26952738 reads; of these: 26952738 (100.00%) were unpaired; of these: 1276037 (4.73%) aligned 0 times 13817552 (51.27%) aligned exactly 1 time 11859149 (44.00%) aligned >1 times 95.27% overall alignment rate Time searching: 00:11:44 Overall time: 00:11:44 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] 13107087 / 25676701 = 0.5105 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 09:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.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 09:55:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:22: 1000000 INFO @ Tue, 16 Jun 2020 09:55:27: 2000000 INFO @ Tue, 16 Jun 2020 09:55:32: 3000000 INFO @ Tue, 16 Jun 2020 09:55:38: 4000000 INFO @ Tue, 16 Jun 2020 09:55:43: 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 09:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.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 09:55:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:48: 6000000 INFO @ Tue, 16 Jun 2020 09:55:52: 1000000 INFO @ Tue, 16 Jun 2020 09:55:54: 7000000 INFO @ Tue, 16 Jun 2020 09:55:58: 2000000 INFO @ Tue, 16 Jun 2020 09:55:59: 8000000 INFO @ Tue, 16 Jun 2020 09:56:03: 3000000 INFO @ Tue, 16 Jun 2020 09:56:05: 9000000 INFO @ Tue, 16 Jun 2020 09:56:09: 4000000 INFO @ Tue, 16 Jun 2020 09:56:10: 10000000 INFO @ Tue, 16 Jun 2020 09:56:14: 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 09:56:16: 11000000 INFO @ Tue, 16 Jun 2020 09:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.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 09:56:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:20: 6000000 INFO @ Tue, 16 Jun 2020 09:56:21: 12000000 INFO @ Tue, 16 Jun 2020 09:56:22: 1000000 INFO @ Tue, 16 Jun 2020 09:56:24: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:56:24: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:56:24: #1 total tags in treatment: 12569614 INFO @ Tue, 16 Jun 2020 09:56:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:24: #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 09:56:25: #1 tags after filtering in treatment: 12569614 INFO @ Tue, 16 Jun 2020 09:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:25: 7000000 INFO @ Tue, 16 Jun 2020 09:56:26: #2 number of paired peaks: 1026 INFO @ Tue, 16 Jun 2020 09:56:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:26: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 09:56:26: #2 alternative fragment length(s) may be 4,134 bps INFO @ Tue, 16 Jun 2020 09:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.05_model.r WARNING @ Tue, 16 Jun 2020 09:56:26: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:26: #2 You may need to consider one of the other alternative d(s): 4,134 WARNING @ Tue, 16 Jun 2020 09:56:26: #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 09:56:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:28: 2000000 INFO @ Tue, 16 Jun 2020 09:56:31: 8000000 INFO @ Tue, 16 Jun 2020 09:56:33: 3000000 INFO @ Tue, 16 Jun 2020 09:56:36: 9000000 INFO @ Tue, 16 Jun 2020 09:56:39: 4000000 INFO @ Tue, 16 Jun 2020 09:56:41: 10000000 INFO @ Tue, 16 Jun 2020 09:56:44: 5000000 INFO @ Tue, 16 Jun 2020 09:56:47: 11000000 INFO @ Tue, 16 Jun 2020 09:56:50: 6000000 INFO @ Tue, 16 Jun 2020 09:56:52: 12000000 INFO @ Tue, 16 Jun 2020 09:56:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:55: 7000000 INFO @ Tue, 16 Jun 2020 09:56:55: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:56:55: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:56:55: #1 total tags in treatment: 12569614 INFO @ Tue, 16 Jun 2020 09:56:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:55: #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 09:56:55: #1 tags after filtering in treatment: 12569614 INFO @ Tue, 16 Jun 2020 09:56:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:56: #2 number of paired peaks: 1026 INFO @ Tue, 16 Jun 2020 09:56:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:56: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 09:56:56: #2 alternative fragment length(s) may be 4,134 bps INFO @ Tue, 16 Jun 2020 09:56:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.10_model.r WARNING @ Tue, 16 Jun 2020 09:56:56: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:56: #2 You may need to consider one of the other alternative d(s): 4,134 WARNING @ Tue, 16 Jun 2020 09:56:56: #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 09:56:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:00: 8000000 INFO @ Tue, 16 Jun 2020 09:57:06: 9000000 INFO @ Tue, 16 Jun 2020 09:57:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.05_summits.bed INFO @ Tue, 16 Jun 2020 09:57:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3009 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:11: 10000000 INFO @ Tue, 16 Jun 2020 09:57:16: 11000000 INFO @ Tue, 16 Jun 2020 09:57:21: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:57:24: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:57:24: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:57:24: #1 total tags in treatment: 12569614 INFO @ Tue, 16 Jun 2020 09:57:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:24: #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 09:57:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:25: #1 tags after filtering in treatment: 12569614 INFO @ Tue, 16 Jun 2020 09:57:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:26: #2 number of paired peaks: 1026 INFO @ Tue, 16 Jun 2020 09:57:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:26: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 09:57:26: #2 alternative fragment length(s) may be 4,134 bps INFO @ Tue, 16 Jun 2020 09:57:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.20_model.r WARNING @ Tue, 16 Jun 2020 09:57:26: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:26: #2 You may need to consider one of the other alternative d(s): 4,134 WARNING @ Tue, 16 Jun 2020 09:57:26: #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 09:57:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.10_summits.bed INFO @ Tue, 16 Jun 2020 09:57:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1523 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:57:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7971791/SRX7971791.20_summits.bed INFO @ Tue, 16 Jun 2020 09:58:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (768 records, 4 fields): 4 millis CompletedMACS2peakCalling