Job ID = 6368179 SRX = SRX494863 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:13:05 prefetch.2.10.7: 1) Downloading 'SRR1198395'... 2020-06-16T00:13:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:15:23 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:15:23 prefetch.2.10.7: 1) 'SRR1198395' was downloaded successfully Read 15695316 spots for SRR1198395/SRR1198395.sra Written 15695316 spots for SRR1198395/SRR1198395.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:27 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1826688 (11.64%) aligned 0 times 11335249 (72.22%) aligned exactly 1 time 2533379 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 1282409 / 13868628 = 0.0925 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 09:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.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 09:23:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:43: 1000000 INFO @ Tue, 16 Jun 2020 09:23:49: 2000000 INFO @ Tue, 16 Jun 2020 09:23:55: 3000000 INFO @ Tue, 16 Jun 2020 09:24:01: 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 09:24:07: 5000000 INFO @ Tue, 16 Jun 2020 09:24:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.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 09:24:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:13: 6000000 INFO @ Tue, 16 Jun 2020 09:24:14: 1000000 INFO @ Tue, 16 Jun 2020 09:24:20: 7000000 INFO @ Tue, 16 Jun 2020 09:24:21: 2000000 INFO @ Tue, 16 Jun 2020 09:24:26: 8000000 INFO @ Tue, 16 Jun 2020 09:24:28: 3000000 INFO @ Tue, 16 Jun 2020 09:24:33: 9000000 INFO @ Tue, 16 Jun 2020 09:24:35: 4000000 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 09:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.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 09:24:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:40: 10000000 INFO @ Tue, 16 Jun 2020 09:24:42: 5000000 INFO @ Tue, 16 Jun 2020 09:24:45: 1000000 INFO @ Tue, 16 Jun 2020 09:24:46: 11000000 INFO @ Tue, 16 Jun 2020 09:24:48: 6000000 INFO @ Tue, 16 Jun 2020 09:24:52: 2000000 INFO @ Tue, 16 Jun 2020 09:24:53: 12000000 INFO @ Tue, 16 Jun 2020 09:24:55: 7000000 INFO @ Tue, 16 Jun 2020 09:24:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:24:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:24:57: #1 total tags in treatment: 12586219 INFO @ Tue, 16 Jun 2020 09:24:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:57: #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 09:24:57: #1 tags after filtering in treatment: 12586219 INFO @ Tue, 16 Jun 2020 09:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:58: #2 number of paired peaks: 333 WARNING @ Tue, 16 Jun 2020 09:24:58: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:58: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:24:58: #2 alternative fragment length(s) may be 2,48,559 bps INFO @ Tue, 16 Jun 2020 09:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.05_model.r WARNING @ Tue, 16 Jun 2020 09:24:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:24:58: #2 You may need to consider one of the other alternative d(s): 2,48,559 WARNING @ Tue, 16 Jun 2020 09:24:58: #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 09:24:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:59: 3000000 INFO @ Tue, 16 Jun 2020 09:25:02: 8000000 INFO @ Tue, 16 Jun 2020 09:25:06: 4000000 INFO @ Tue, 16 Jun 2020 09:25:09: 9000000 INFO @ Tue, 16 Jun 2020 09:25:13: 5000000 INFO @ Tue, 16 Jun 2020 09:25:16: 10000000 INFO @ Tue, 16 Jun 2020 09:25:20: 6000000 INFO @ Tue, 16 Jun 2020 09:25:22: 11000000 INFO @ Tue, 16 Jun 2020 09:25:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:27: 7000000 INFO @ Tue, 16 Jun 2020 09:25:29: 12000000 INFO @ Tue, 16 Jun 2020 09:25:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:25:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:25:33: #1 total tags in treatment: 12586219 INFO @ Tue, 16 Jun 2020 09:25:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:33: #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 09:25:33: #1 tags after filtering in treatment: 12586219 INFO @ Tue, 16 Jun 2020 09:25:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:34: 8000000 INFO @ Tue, 16 Jun 2020 09:25:34: #2 number of paired peaks: 333 WARNING @ Tue, 16 Jun 2020 09:25:34: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:34: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:25:34: #2 alternative fragment length(s) may be 2,48,559 bps INFO @ Tue, 16 Jun 2020 09:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.10_model.r WARNING @ Tue, 16 Jun 2020 09:25:34: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:34: #2 You may need to consider one of the other alternative d(s): 2,48,559 WARNING @ Tue, 16 Jun 2020 09:25:34: #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 09:25:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (673 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:25:40: 9000000 INFO @ Tue, 16 Jun 2020 09:25:46: 10000000 INFO @ Tue, 16 Jun 2020 09:25:53: 11000000 INFO @ Tue, 16 Jun 2020 09:26:00: 12000000 INFO @ Tue, 16 Jun 2020 09:26:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:26:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:26:03: #1 total tags in treatment: 12586219 INFO @ Tue, 16 Jun 2020 09:26:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:03: #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 09:26:04: #1 tags after filtering in treatment: 12586219 INFO @ Tue, 16 Jun 2020 09:26:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:04: #2 number of paired peaks: 333 WARNING @ Tue, 16 Jun 2020 09:26:04: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:05: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:26:05: #2 alternative fragment length(s) may be 2,48,559 bps INFO @ Tue, 16 Jun 2020 09:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.20_model.r WARNING @ Tue, 16 Jun 2020 09:26:05: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:05: #2 You may need to consider one of the other alternative d(s): 2,48,559 WARNING @ Tue, 16 Jun 2020 09:26:05: #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 09:26:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:26:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494863/SRX494863.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 1 millis CompletedMACS2peakCalling