Job ID = 6367925 SRX = SRX4200534 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:19 prefetch.2.10.7: 1) Downloading 'SRR7298000'... 2020-06-16T00:06:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:08:05 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:08:06 prefetch.2.10.7: 'SRR7298000' is valid 2020-06-16T00:08:06 prefetch.2.10.7: 1) 'SRR7298000' was downloaded successfully 2020-06-16T00:08:06 prefetch.2.10.7: 'SRR7298000' has 0 unresolved dependencies Read 18300137 spots for SRR7298000/SRR7298000.sra Written 18300137 spots for SRR7298000/SRR7298000.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: 00:04:20 18300137 reads; of these: 18300137 (100.00%) were unpaired; of these: 1053685 (5.76%) aligned 0 times 15173980 (82.92%) aligned exactly 1 time 2072472 (11.32%) aligned >1 times 94.24% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 12257158 / 17246452 = 0.7107 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 09:16:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.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 09:16:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:32: 1000000 INFO @ Tue, 16 Jun 2020 09:16:37: 2000000 INFO @ Tue, 16 Jun 2020 09:16:43: 3000000 INFO @ Tue, 16 Jun 2020 09:16:49: 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 @ Tue, 16 Jun 2020 09:16:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:54: #1 total tags in treatment: 4989294 INFO @ Tue, 16 Jun 2020 09:16:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:54: #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 09:16:54: #1 tags after filtering in treatment: 4989294 INFO @ Tue, 16 Jun 2020 09:16:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:55: #2 number of paired peaks: 160 WARNING @ Tue, 16 Jun 2020 09:16:55: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:55: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 09:16:55: #2 alternative fragment length(s) may be 4,60,96,510,569,591 bps INFO @ Tue, 16 Jun 2020 09:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:55: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:55: #2 You may need to consider one of the other alternative d(s): 4,60,96,510,569,591 WARNING @ Tue, 16 Jun 2020 09:16:55: #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 09:16:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.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 09:16:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:01: 1000000 INFO @ Tue, 16 Jun 2020 09:17:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:07: 2000000 INFO @ Tue, 16 Jun 2020 09:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.05_summits.bed INFO @ Tue, 16 Jun 2020 09:17:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (326 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:12: 3000000 INFO @ Tue, 16 Jun 2020 09:17:18: 4000000 INFO @ Tue, 16 Jun 2020 09:17:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:23: #1 total tags in treatment: 4989294 INFO @ Tue, 16 Jun 2020 09:17:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:23: #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 09:17:23: #1 tags after filtering in treatment: 4989294 INFO @ Tue, 16 Jun 2020 09:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:24: #2 number of paired peaks: 160 WARNING @ Tue, 16 Jun 2020 09:17:24: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:24: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 09:17:24: #2 alternative fragment length(s) may be 4,60,96,510,569,591 bps INFO @ Tue, 16 Jun 2020 09:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.10_model.r WARNING @ Tue, 16 Jun 2020 09:17:24: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:24: #2 You may need to consider one of the other alternative d(s): 4,60,96,510,569,591 WARNING @ Tue, 16 Jun 2020 09:17:24: #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 09:17:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:24: #3 Pre-compute pvalue-qvalue table... 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 09:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.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 09:17:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:31: 1000000 INFO @ Tue, 16 Jun 2020 09:17:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:37: 2000000 INFO @ Tue, 16 Jun 2020 09:17:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (85 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:17:48: 4000000 INFO @ Tue, 16 Jun 2020 09:17:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:53: #1 total tags in treatment: 4989294 INFO @ Tue, 16 Jun 2020 09:17:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:53: #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 09:17:53: #1 tags after filtering in treatment: 4989294 INFO @ Tue, 16 Jun 2020 09:17:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:54: #2 number of paired peaks: 160 WARNING @ Tue, 16 Jun 2020 09:17:54: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:54: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 09:17:54: #2 alternative fragment length(s) may be 4,60,96,510,569,591 bps INFO @ Tue, 16 Jun 2020 09:17:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:54: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:54: #2 You may need to consider one of the other alternative d(s): 4,60,96,510,569,591 WARNING @ Tue, 16 Jun 2020 09:17:54: #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 09:17:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:18:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4200534/SRX4200534.20_summits.bed INFO @ Tue, 16 Jun 2020 09:18:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling