Job ID = 6366834 SRX = SRX2350733 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:04:08 prefetch.2.10.7: 1) Downloading 'SRR5024042'... 2020-06-15T23:04:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:33 prefetch.2.10.7: 1) 'SRR5024042' was downloaded successfully Read 13574890 spots for SRR5024042/SRR5024042.sra Written 13574890 spots for SRR5024042/SRR5024042.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: 00:03:13 13574890 reads; of these: 13574890 (100.00%) were unpaired; of these: 279032 (2.06%) aligned 0 times 10524101 (77.53%) aligned exactly 1 time 2771757 (20.42%) aligned >1 times 97.94% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 1677348 / 13295858 = 0.1262 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 08:13:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.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 08:13:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:07: 1000000 INFO @ Tue, 16 Jun 2020 08:13:13: 2000000 INFO @ Tue, 16 Jun 2020 08:13:20: 3000000 INFO @ Tue, 16 Jun 2020 08:13:27: 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 08:13:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.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 08:13:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:34: 5000000 INFO @ Tue, 16 Jun 2020 08:13:37: 1000000 INFO @ Tue, 16 Jun 2020 08:13:41: 6000000 INFO @ Tue, 16 Jun 2020 08:13:45: 2000000 INFO @ Tue, 16 Jun 2020 08:13:49: 7000000 INFO @ Tue, 16 Jun 2020 08:13:52: 3000000 INFO @ Tue, 16 Jun 2020 08:13:57: 8000000 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 08:13:59: 4000000 INFO @ Tue, 16 Jun 2020 08:14:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.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 08:14:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:05: 9000000 INFO @ Tue, 16 Jun 2020 08:14:07: 5000000 INFO @ Tue, 16 Jun 2020 08:14:07: 1000000 INFO @ Tue, 16 Jun 2020 08:14:12: 10000000 INFO @ Tue, 16 Jun 2020 08:14:14: 6000000 INFO @ Tue, 16 Jun 2020 08:14:14: 2000000 INFO @ Tue, 16 Jun 2020 08:14:20: 11000000 INFO @ Tue, 16 Jun 2020 08:14:21: 7000000 INFO @ Tue, 16 Jun 2020 08:14:21: 3000000 INFO @ Tue, 16 Jun 2020 08:14:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:24: #1 total tags in treatment: 11618510 INFO @ Tue, 16 Jun 2020 08:14:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:24: #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 08:14:24: #1 tags after filtering in treatment: 11618510 INFO @ Tue, 16 Jun 2020 08:14:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:25: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 08:14:25: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:25: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:14:25: #2 alternative fragment length(s) may be 2,48,575 bps INFO @ Tue, 16 Jun 2020 08:14:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.05_model.r WARNING @ Tue, 16 Jun 2020 08:14:25: #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 08:14:25: #2 You may need to consider one of the other alternative d(s): 2,48,575 WARNING @ Tue, 16 Jun 2020 08:14:25: #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 08:14:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:28: 8000000 INFO @ Tue, 16 Jun 2020 08:14:28: 4000000 INFO @ Tue, 16 Jun 2020 08:14:35: 9000000 INFO @ Tue, 16 Jun 2020 08:14:35: 5000000 INFO @ Tue, 16 Jun 2020 08:14:42: 6000000 INFO @ Tue, 16 Jun 2020 08:14:42: 10000000 INFO @ Tue, 16 Jun 2020 08:14:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:49: 7000000 INFO @ Tue, 16 Jun 2020 08:14:49: 11000000 INFO @ Tue, 16 Jun 2020 08:14:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:53: #1 total tags in treatment: 11618510 INFO @ Tue, 16 Jun 2020 08:14:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:53: #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 08:14:54: #1 tags after filtering in treatment: 11618510 INFO @ Tue, 16 Jun 2020 08:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:54: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 08:14:54: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:54: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:14:54: #2 alternative fragment length(s) may be 2,48,575 bps INFO @ Tue, 16 Jun 2020 08:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.10_model.r WARNING @ Tue, 16 Jun 2020 08:14:54: #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 08:14:54: #2 You may need to consider one of the other alternative d(s): 2,48,575 WARNING @ Tue, 16 Jun 2020 08:14:54: #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 08:14:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:56: 8000000 INFO @ Tue, 16 Jun 2020 08:14:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (721 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:02: 9000000 INFO @ Tue, 16 Jun 2020 08:15:08: 10000000 INFO @ Tue, 16 Jun 2020 08:15:15: 11000000 INFO @ Tue, 16 Jun 2020 08:15:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:18: #1 total tags in treatment: 11618510 INFO @ Tue, 16 Jun 2020 08:15:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:18: #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 08:15:19: #1 tags after filtering in treatment: 11618510 INFO @ Tue, 16 Jun 2020 08:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:19: #2 number of paired peaks: 397 WARNING @ Tue, 16 Jun 2020 08:15:19: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:19: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:15:19: #2 alternative fragment length(s) may be 2,48,575 bps INFO @ Tue, 16 Jun 2020 08:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.20_model.r WARNING @ Tue, 16 Jun 2020 08:15:19: #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 08:15:19: #2 You may need to consider one of the other alternative d(s): 2,48,575 WARNING @ Tue, 16 Jun 2020 08:15:19: #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 08:15:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (474 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350733/SRX2350733.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (207 records, 4 fields): 1 millis CompletedMACS2peakCalling