Job ID = 6366760 SRX = SRX2228913 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:50:56 prefetch.2.10.7: 1) Downloading 'SRR4380369'... 2020-06-15T22:50:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:52:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:52:55 prefetch.2.10.7: 1) 'SRR4380369' was downloaded successfully Read 16440500 spots for SRR4380369/SRR4380369.sra Written 16440500 spots for SRR4380369/SRR4380369.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: 00:03:53 16440500 reads; of these: 16440500 (100.00%) were unpaired; of these: 137993 (0.84%) aligned 0 times 13513255 (82.19%) aligned exactly 1 time 2789252 (16.97%) aligned >1 times 99.16% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 1797343 / 16302507 = 0.1102 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 08:02:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.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 08:02:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:32: 1000000 INFO @ Tue, 16 Jun 2020 08:02:38: 2000000 INFO @ Tue, 16 Jun 2020 08:02:43: 3000000 INFO @ Tue, 16 Jun 2020 08:02:49: 4000000 INFO @ Tue, 16 Jun 2020 08:02:54: 5000000 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 08:02:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.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 08:02:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:00: 6000000 INFO @ Tue, 16 Jun 2020 08:03:02: 1000000 INFO @ Tue, 16 Jun 2020 08:03:05: 7000000 INFO @ Tue, 16 Jun 2020 08:03:08: 2000000 INFO @ Tue, 16 Jun 2020 08:03:11: 8000000 INFO @ Tue, 16 Jun 2020 08:03:14: 3000000 INFO @ Tue, 16 Jun 2020 08:03:17: 9000000 INFO @ Tue, 16 Jun 2020 08:03:19: 4000000 INFO @ Tue, 16 Jun 2020 08:03:22: 10000000 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 08:03:25: 5000000 INFO @ Tue, 16 Jun 2020 08:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.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 08:03:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:28: 11000000 INFO @ Tue, 16 Jun 2020 08:03:31: 6000000 INFO @ Tue, 16 Jun 2020 08:03:32: 1000000 INFO @ Tue, 16 Jun 2020 08:03:34: 12000000 INFO @ Tue, 16 Jun 2020 08:03:37: 7000000 INFO @ Tue, 16 Jun 2020 08:03:38: 2000000 INFO @ Tue, 16 Jun 2020 08:03:39: 13000000 INFO @ Tue, 16 Jun 2020 08:03:42: 8000000 INFO @ Tue, 16 Jun 2020 08:03:44: 3000000 INFO @ Tue, 16 Jun 2020 08:03:45: 14000000 INFO @ Tue, 16 Jun 2020 08:03:48: 9000000 INFO @ Tue, 16 Jun 2020 08:03:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:03:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:03:48: #1 total tags in treatment: 14505164 INFO @ Tue, 16 Jun 2020 08:03:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:48: #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 08:03:48: #1 tags after filtering in treatment: 14505164 INFO @ Tue, 16 Jun 2020 08:03:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:50: #2 number of paired peaks: 338 WARNING @ Tue, 16 Jun 2020 08:03:50: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:50: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:03:50: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 08:03:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.05_model.r WARNING @ Tue, 16 Jun 2020 08:03:50: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:50: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 08:03:50: #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 08:03:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:50: 4000000 INFO @ Tue, 16 Jun 2020 08:03:54: 10000000 INFO @ Tue, 16 Jun 2020 08:03:56: 5000000 INFO @ Tue, 16 Jun 2020 08:03:59: 11000000 INFO @ Tue, 16 Jun 2020 08:04:01: 6000000 INFO @ Tue, 16 Jun 2020 08:04:05: 12000000 INFO @ Tue, 16 Jun 2020 08:04:07: 7000000 INFO @ Tue, 16 Jun 2020 08:04:11: 13000000 INFO @ Tue, 16 Jun 2020 08:04:12: 8000000 INFO @ Tue, 16 Jun 2020 08:04:16: 14000000 INFO @ Tue, 16 Jun 2020 08:04:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:18: 9000000 INFO @ Tue, 16 Jun 2020 08:04:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:04:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:04:19: #1 total tags in treatment: 14505164 INFO @ Tue, 16 Jun 2020 08:04:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:19: #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 08:04:19: #1 tags after filtering in treatment: 14505164 INFO @ Tue, 16 Jun 2020 08:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:20: #2 number of paired peaks: 338 WARNING @ Tue, 16 Jun 2020 08:04:20: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:20: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:04:20: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 08:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.10_model.r WARNING @ Tue, 16 Jun 2020 08:04:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:21: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 08:04:21: #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 08:04:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:24: 10000000 INFO @ Tue, 16 Jun 2020 08:04:29: 11000000 INFO @ Tue, 16 Jun 2020 08:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (704 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:34: 12000000 INFO @ Tue, 16 Jun 2020 08:04:40: 13000000 INFO @ Tue, 16 Jun 2020 08:04:45: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:04:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:04:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:04:48: #1 total tags in treatment: 14505164 INFO @ Tue, 16 Jun 2020 08:04:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:48: #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 08:04:48: #1 tags after filtering in treatment: 14505164 INFO @ Tue, 16 Jun 2020 08:04:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:49: #2 number of paired peaks: 338 WARNING @ Tue, 16 Jun 2020 08:04:49: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:49: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:04:49: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 08:04:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.20_model.r WARNING @ Tue, 16 Jun 2020 08:04:49: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:49: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 08:04:49: #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 08:04:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.10_summits.bed INFO @ Tue, 16 Jun 2020 08:05:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (507 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228913/SRX2228913.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 1 millis CompletedMACS2peakCalling