Job ID = 6366730 SRX = SRX2228883 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:11 prefetch.2.10.7: 1) Downloading 'SRR4380339'... 2020-06-15T22:54:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:55:00 prefetch.2.10.7: 'SRR4380339' is valid 2020-06-15T22:55:00 prefetch.2.10.7: 1) 'SRR4380339' was downloaded successfully 2020-06-15T22:55:00 prefetch.2.10.7: 'SRR4380339' has 0 unresolved dependencies Read 18646407 spots for SRR4380339/SRR4380339.sra Written 18646407 spots for SRR4380339/SRR4380339.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: 00:02:50 18646407 reads; of these: 18646407 (100.00%) were unpaired; of these: 11134616 (59.71%) aligned 0 times 6038362 (32.38%) aligned exactly 1 time 1473429 (7.90%) aligned >1 times 40.29% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 1095677 / 7511791 = 0.1459 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 08:01:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.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 08:01:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:24: 1000000 INFO @ Tue, 16 Jun 2020 08:01:30: 2000000 INFO @ Tue, 16 Jun 2020 08:01:37: 3000000 INFO @ Tue, 16 Jun 2020 08:01:43: 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 08:01:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.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 08:01:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:49: 5000000 INFO @ Tue, 16 Jun 2020 08:01:55: 1000000 INFO @ Tue, 16 Jun 2020 08:01:55: 6000000 INFO @ Tue, 16 Jun 2020 08:01:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:01:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:01:58: #1 total tags in treatment: 6416114 INFO @ Tue, 16 Jun 2020 08:01:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:01:58: #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 08:01:58: #1 tags after filtering in treatment: 6416114 INFO @ Tue, 16 Jun 2020 08:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:01:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:01:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:01:59: #2 number of paired peaks: 496 WARNING @ Tue, 16 Jun 2020 08:01:59: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Tue, 16 Jun 2020 08:01:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:01:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:01:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:01:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:01:59: #2 predicted fragment length is 65 bps INFO @ Tue, 16 Jun 2020 08:01:59: #2 alternative fragment length(s) may be 65 bps INFO @ Tue, 16 Jun 2020 08:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.05_model.r WARNING @ Tue, 16 Jun 2020 08:01:59: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:01:59: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Tue, 16 Jun 2020 08:01:59: #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 08:01:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:01: 2000000 INFO @ Tue, 16 Jun 2020 08:02:07: 3000000 INFO @ Tue, 16 Jun 2020 08:02:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:14: 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 08:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.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 08:02:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:20: 5000000 INFO @ Tue, 16 Jun 2020 08:02:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.05_summits.bed INFO @ Tue, 16 Jun 2020 08:02:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (785 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:02:25: 1000000 INFO @ Tue, 16 Jun 2020 08:02:27: 6000000 INFO @ Tue, 16 Jun 2020 08:02:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:30: #1 total tags in treatment: 6416114 INFO @ Tue, 16 Jun 2020 08:02:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:30: #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 08:02:30: #1 tags after filtering in treatment: 6416114 INFO @ Tue, 16 Jun 2020 08:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:30: #2 number of paired peaks: 496 WARNING @ Tue, 16 Jun 2020 08:02:30: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:30: #2 predicted fragment length is 65 bps INFO @ Tue, 16 Jun 2020 08:02:30: #2 alternative fragment length(s) may be 65 bps INFO @ Tue, 16 Jun 2020 08:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.10_model.r WARNING @ Tue, 16 Jun 2020 08:02:30: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:02:30: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Tue, 16 Jun 2020 08:02:30: #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 08:02:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:32: 2000000 INFO @ Tue, 16 Jun 2020 08:02:38: 3000000 INFO @ Tue, 16 Jun 2020 08:02:44: 4000000 INFO @ Tue, 16 Jun 2020 08:02:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:50: 5000000 INFO @ Tue, 16 Jun 2020 08:02:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:02:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:02:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.10_summits.bed INFO @ Tue, 16 Jun 2020 08:02:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (526 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:02:57: 6000000 INFO @ Tue, 16 Jun 2020 08:02:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:02:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:02:59: #1 total tags in treatment: 6416114 INFO @ Tue, 16 Jun 2020 08:02:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:59: #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 08:02:59: #1 tags after filtering in treatment: 6416114 INFO @ Tue, 16 Jun 2020 08:02:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:00: #2 number of paired peaks: 496 WARNING @ Tue, 16 Jun 2020 08:03:00: Fewer paired peaks (496) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 496 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:00: #2 predicted fragment length is 65 bps INFO @ Tue, 16 Jun 2020 08:03:00: #2 alternative fragment length(s) may be 65 bps INFO @ Tue, 16 Jun 2020 08:03:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.20_model.r WARNING @ Tue, 16 Jun 2020 08:03:00: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:00: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Tue, 16 Jun 2020 08:03:00: #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 08:03:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228883/SRX2228883.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling