Job ID = 6366105 SRX = SRX063962 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:23 prefetch.2.10.7: 1) Downloading 'SRR210890'... 2020-06-15T22:57:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:58:49 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:58:49 prefetch.2.10.7: 1) 'SRR210890' was downloaded successfully Read 19120178 spots for SRR210890/SRR210890.sra Written 19120178 spots for SRR210890/SRR210890.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: 00:03:43 19120178 reads; of these: 19120178 (100.00%) were unpaired; of these: 304345 (1.59%) aligned 0 times 15531558 (81.23%) aligned exactly 1 time 3284275 (17.18%) aligned >1 times 98.41% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 1969799 / 18815833 = 0.1047 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 08:08:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.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 08:08:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:41: 1000000 INFO @ Tue, 16 Jun 2020 08:08:46: 2000000 INFO @ Tue, 16 Jun 2020 08:08:52: 3000000 INFO @ Tue, 16 Jun 2020 08:08:58: 4000000 INFO @ Tue, 16 Jun 2020 08:09:03: 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 08:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.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 08:09:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:09: 6000000 INFO @ Tue, 16 Jun 2020 08:09:11: 1000000 INFO @ Tue, 16 Jun 2020 08:09:15: 7000000 INFO @ Tue, 16 Jun 2020 08:09:17: 2000000 INFO @ Tue, 16 Jun 2020 08:09:21: 8000000 INFO @ Tue, 16 Jun 2020 08:09:22: 3000000 INFO @ Tue, 16 Jun 2020 08:09:27: 9000000 INFO @ Tue, 16 Jun 2020 08:09:28: 4000000 INFO @ Tue, 16 Jun 2020 08:09:33: 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 08:09:34: 5000000 INFO @ Tue, 16 Jun 2020 08:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.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 08:09:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:38: 11000000 INFO @ Tue, 16 Jun 2020 08:09:40: 6000000 INFO @ Tue, 16 Jun 2020 08:09:41: 1000000 INFO @ Tue, 16 Jun 2020 08:09:44: 12000000 INFO @ Tue, 16 Jun 2020 08:09:46: 7000000 INFO @ Tue, 16 Jun 2020 08:09:47: 2000000 INFO @ Tue, 16 Jun 2020 08:09:50: 13000000 INFO @ Tue, 16 Jun 2020 08:09:52: 8000000 INFO @ Tue, 16 Jun 2020 08:09:53: 3000000 INFO @ Tue, 16 Jun 2020 08:09:56: 14000000 INFO @ Tue, 16 Jun 2020 08:09:57: 9000000 INFO @ Tue, 16 Jun 2020 08:09:59: 4000000 INFO @ Tue, 16 Jun 2020 08:10:03: 15000000 INFO @ Tue, 16 Jun 2020 08:10:04: 10000000 INFO @ Tue, 16 Jun 2020 08:10:05: 5000000 INFO @ Tue, 16 Jun 2020 08:10:09: 16000000 INFO @ Tue, 16 Jun 2020 08:10:10: 11000000 INFO @ Tue, 16 Jun 2020 08:10:12: 6000000 INFO @ Tue, 16 Jun 2020 08:10:14: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:10:14: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:10:14: #1 total tags in treatment: 16846034 INFO @ Tue, 16 Jun 2020 08:10:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:14: #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 08:10:14: #1 tags after filtering in treatment: 16846034 INFO @ Tue, 16 Jun 2020 08:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:15: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 08:10:15: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:16: 12000000 INFO @ Tue, 16 Jun 2020 08:10:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:16: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:10:16: #2 alternative fragment length(s) may be 1,38,505,576,598 bps INFO @ Tue, 16 Jun 2020 08:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.05_model.r WARNING @ Tue, 16 Jun 2020 08:10:16: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:16: #2 You may need to consider one of the other alternative d(s): 1,38,505,576,598 WARNING @ Tue, 16 Jun 2020 08:10:16: #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 08:10:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:18: 7000000 INFO @ Tue, 16 Jun 2020 08:10:22: 13000000 INFO @ Tue, 16 Jun 2020 08:10:24: 8000000 INFO @ Tue, 16 Jun 2020 08:10:28: 14000000 INFO @ Tue, 16 Jun 2020 08:10:30: 9000000 INFO @ Tue, 16 Jun 2020 08:10:34: 15000000 INFO @ Tue, 16 Jun 2020 08:10:36: 10000000 INFO @ Tue, 16 Jun 2020 08:10:40: 16000000 INFO @ Tue, 16 Jun 2020 08:10:42: 11000000 INFO @ Tue, 16 Jun 2020 08:10:45: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:10:45: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:10:45: #1 total tags in treatment: 16846034 INFO @ Tue, 16 Jun 2020 08:10:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:45: #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 08:10:45: #1 tags after filtering in treatment: 16846034 INFO @ Tue, 16 Jun 2020 08:10:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:47: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 08:10:47: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:47: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:10:47: #2 alternative fragment length(s) may be 1,38,505,576,598 bps INFO @ Tue, 16 Jun 2020 08:10:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.10_model.r WARNING @ Tue, 16 Jun 2020 08:10:47: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:47: #2 You may need to consider one of the other alternative d(s): 1,38,505,576,598 WARNING @ Tue, 16 Jun 2020 08:10:47: #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 08:10:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:48: 12000000 INFO @ Tue, 16 Jun 2020 08:10:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:54: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:00: 14000000 INFO @ Tue, 16 Jun 2020 08:11:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:05: 15000000 INFO @ Tue, 16 Jun 2020 08:11:11: 16000000 INFO @ Tue, 16 Jun 2020 08:11:16: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:11:16: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:11:16: #1 total tags in treatment: 16846034 INFO @ Tue, 16 Jun 2020 08:11:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:16: #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 08:11:16: #1 tags after filtering in treatment: 16846034 INFO @ Tue, 16 Jun 2020 08:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:18: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 08:11:18: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:18: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:11:18: #2 alternative fragment length(s) may be 1,38,505,576,598 bps INFO @ Tue, 16 Jun 2020 08:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.20_model.r WARNING @ Tue, 16 Jun 2020 08:11:18: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:18: #2 You may need to consider one of the other alternative d(s): 1,38,505,576,598 WARNING @ Tue, 16 Jun 2020 08:11:18: #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 08:11:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.10_summits.bed INFO @ Tue, 16 Jun 2020 08:11:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX063962/SRX063962.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (94 records, 4 fields): 1 millis CompletedMACS2peakCalling