Job ID = 6368219 SRX = SRX494902 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:07:39 prefetch.2.10.7: 1) Downloading 'SRR1198434'... 2020-06-16T00:07:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:10:25 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:10:25 prefetch.2.10.7: 1) 'SRR1198434' was downloaded successfully Read 15695316 spots for SRR1198434/SRR1198434.sra Written 15695316 spots for SRR1198434/SRR1198434.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: 00:03:40 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1826667 (11.64%) aligned 0 times 11335272 (72.22%) aligned exactly 1 time 2533377 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 1281766 / 13868649 = 0.0924 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 09:18:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.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 09:18:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:02: 1000000 INFO @ Tue, 16 Jun 2020 09:19:07: 2000000 INFO @ Tue, 16 Jun 2020 09:19:13: 3000000 INFO @ Tue, 16 Jun 2020 09:19:19: 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 09:19:24: 5000000 INFO @ Tue, 16 Jun 2020 09:19:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.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 09:19:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:30: 6000000 INFO @ Tue, 16 Jun 2020 09:19:32: 1000000 INFO @ Tue, 16 Jun 2020 09:19:37: 7000000 INFO @ Tue, 16 Jun 2020 09:19:39: 2000000 INFO @ Tue, 16 Jun 2020 09:19:43: 8000000 INFO @ Tue, 16 Jun 2020 09:19:45: 3000000 INFO @ Tue, 16 Jun 2020 09:19:49: 9000000 INFO @ Tue, 16 Jun 2020 09:19:51: 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 09:19:56: 10000000 INFO @ Tue, 16 Jun 2020 09:19:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.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 09:19:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:57: 5000000 INFO @ Tue, 16 Jun 2020 09:20:02: 11000000 INFO @ Tue, 16 Jun 2020 09:20:03: 1000000 INFO @ Tue, 16 Jun 2020 09:20:04: 6000000 INFO @ Tue, 16 Jun 2020 09:20:09: 12000000 INFO @ Tue, 16 Jun 2020 09:20:09: 2000000 INFO @ Tue, 16 Jun 2020 09:20:11: 7000000 INFO @ Tue, 16 Jun 2020 09:20:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:20:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:20:13: #1 total tags in treatment: 12586883 INFO @ Tue, 16 Jun 2020 09:20:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:13: #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 09:20:13: #1 tags after filtering in treatment: 12586883 INFO @ Tue, 16 Jun 2020 09:20:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:14: #2 number of paired peaks: 352 WARNING @ Tue, 16 Jun 2020 09:20:14: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:14: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:20:14: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 09:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:14: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:14: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 09:20:14: #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 09:20:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:16: 3000000 INFO @ Tue, 16 Jun 2020 09:20:17: 8000000 INFO @ Tue, 16 Jun 2020 09:20:22: 4000000 INFO @ Tue, 16 Jun 2020 09:20:23: 9000000 INFO @ Tue, 16 Jun 2020 09:20:29: 5000000 INFO @ Tue, 16 Jun 2020 09:20:30: 10000000 INFO @ Tue, 16 Jun 2020 09:20:35: 6000000 INFO @ Tue, 16 Jun 2020 09:20:36: 11000000 INFO @ Tue, 16 Jun 2020 09:20:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:41: 7000000 INFO @ Tue, 16 Jun 2020 09:20:42: 12000000 INFO @ Tue, 16 Jun 2020 09:20:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:20:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:20:46: #1 total tags in treatment: 12586883 INFO @ Tue, 16 Jun 2020 09:20:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:46: #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 09:20:46: #1 tags after filtering in treatment: 12586883 INFO @ Tue, 16 Jun 2020 09:20:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:47: #2 number of paired peaks: 352 WARNING @ Tue, 16 Jun 2020 09:20:47: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:47: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:20:47: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 09:20:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:47: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:47: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 09:20:47: #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 09:20:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:48: 8000000 INFO @ Tue, 16 Jun 2020 09:20:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (667 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:54: 9000000 INFO @ Tue, 16 Jun 2020 09:21:00: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:06: 11000000 INFO @ Tue, 16 Jun 2020 09:21:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:12: 12000000 INFO @ Tue, 16 Jun 2020 09:21:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:21:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:21:15: #1 total tags in treatment: 12586883 INFO @ Tue, 16 Jun 2020 09:21:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:15: #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 09:21:15: #1 tags after filtering in treatment: 12586883 INFO @ Tue, 16 Jun 2020 09:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:16: #2 number of paired peaks: 352 WARNING @ Tue, 16 Jun 2020 09:21:16: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:16: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:21:16: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 09:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:16: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 09:21:16: #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 09:21:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (474 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494902/SRX494902.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 1 millis CompletedMACS2peakCalling