Job ID = 6368414 SRX = SRX495093 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:21 prefetch.2.10.7: 1) Downloading 'SRR1198625'... 2020-06-16T00:22:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:38 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:39 prefetch.2.10.7: 'SRR1198625' is valid 2020-06-16T00:23:39 prefetch.2.10.7: 1) 'SRR1198625' was downloaded successfully Read 10075319 spots for SRR1198625/SRR1198625.sra Written 10075319 spots for SRR1198625/SRR1198625.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: 00:01:56 10075319 reads; of these: 10075319 (100.00%) were unpaired; of these: 1468000 (14.57%) aligned 0 times 6959275 (69.07%) aligned exactly 1 time 1648044 (16.36%) aligned >1 times 85.43% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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_rmdupse_core] 1384913 / 8607319 = 0.1609 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 09:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.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 09:28:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:25: 1000000 INFO @ Tue, 16 Jun 2020 09:28:32: 2000000 INFO @ Tue, 16 Jun 2020 09:28:40: 3000000 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 09:28:47: 4000000 INFO @ Tue, 16 Jun 2020 09:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.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 09:28:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:55: 5000000 INFO @ Tue, 16 Jun 2020 09:28:57: 1000000 INFO @ Tue, 16 Jun 2020 09:29:02: 6000000 INFO @ Tue, 16 Jun 2020 09:29:05: 2000000 INFO @ Tue, 16 Jun 2020 09:29:10: 7000000 INFO @ Tue, 16 Jun 2020 09:29:11: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:29:11: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:29:11: #1 total tags in treatment: 7222406 INFO @ Tue, 16 Jun 2020 09:29:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:11: #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 09:29:11: #1 tags after filtering in treatment: 7222406 INFO @ Tue, 16 Jun 2020 09:29:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:12: #2 number of paired peaks: 558 WARNING @ Tue, 16 Jun 2020 09:29:12: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:12: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 09:29:12: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 16 Jun 2020 09:29:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.05_model.r WARNING @ Tue, 16 Jun 2020 09:29:12: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:12: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 16 Jun 2020 09:29:12: #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 09:29:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:13: 3000000 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 09:29:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.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 09:29:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:21: 4000000 INFO @ Tue, 16 Jun 2020 09:29:26: 1000000 INFO @ Tue, 16 Jun 2020 09:29:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:28: 5000000 INFO @ Tue, 16 Jun 2020 09:29:33: 2000000 INFO @ Tue, 16 Jun 2020 09:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1800 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:36: 6000000 INFO @ Tue, 16 Jun 2020 09:29:41: 3000000 INFO @ Tue, 16 Jun 2020 09:29:43: 7000000 INFO @ Tue, 16 Jun 2020 09:29:45: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:29:45: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:29:45: #1 total tags in treatment: 7222406 INFO @ Tue, 16 Jun 2020 09:29:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:45: #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 09:29:45: #1 tags after filtering in treatment: 7222406 INFO @ Tue, 16 Jun 2020 09:29:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:45: #2 number of paired peaks: 558 WARNING @ Tue, 16 Jun 2020 09:29:45: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:45: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 09:29:45: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 16 Jun 2020 09:29:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.10_model.r WARNING @ Tue, 16 Jun 2020 09:29:45: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:45: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 16 Jun 2020 09:29:45: #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 09:29:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:48: 4000000 INFO @ Tue, 16 Jun 2020 09:29:54: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:00: 6000000 INFO @ Tue, 16 Jun 2020 09:30:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:07: 7000000 INFO @ Tue, 16 Jun 2020 09:30:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:08: Done! INFO @ Tue, 16 Jun 2020 09:30:08: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:30:08: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:30:08: #1 total tags in treatment: 7222406 INFO @ Tue, 16 Jun 2020 09:30:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (627 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:08: #1 tags after filtering in treatment: 7222406 INFO @ Tue, 16 Jun 2020 09:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:09: #2 number of paired peaks: 558 WARNING @ Tue, 16 Jun 2020 09:30:09: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:09: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 09:30:09: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 16 Jun 2020 09:30:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.20_model.r WARNING @ Tue, 16 Jun 2020 09:30:09: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:09: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 16 Jun 2020 09:30:09: #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 09:30:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495093/SRX495093.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 1 millis CompletedMACS2peakCalling