Job ID = 6368123 SRX = SRX466586 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:15:22 prefetch.2.10.7: 1) Downloading 'SRR1163652'... 2020-06-16T00:15:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:17:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:17:18 prefetch.2.10.7: 'SRR1163652' is valid 2020-06-16T00:17:18 prefetch.2.10.7: 1) 'SRR1163652' was downloaded successfully Read 18854814 spots for SRR1163652/SRR1163652.sra Written 18854814 spots for SRR1163652/SRR1163652.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: 00:03:47 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 288225 (1.53%) aligned 0 times 14954526 (79.31%) aligned exactly 1 time 3612063 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 3522083 / 18566589 = 0.1897 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 09:26:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.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 09:26:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:19: 1000000 INFO @ Tue, 16 Jun 2020 09:26:24: 2000000 INFO @ Tue, 16 Jun 2020 09:26:29: 3000000 INFO @ Tue, 16 Jun 2020 09:26:34: 4000000 INFO @ Tue, 16 Jun 2020 09:26:39: 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 09:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.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 09:26:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:45: 6000000 INFO @ Tue, 16 Jun 2020 09:26:49: 1000000 INFO @ Tue, 16 Jun 2020 09:26:50: 7000000 INFO @ Tue, 16 Jun 2020 09:26:54: 2000000 INFO @ Tue, 16 Jun 2020 09:26:55: 8000000 INFO @ Tue, 16 Jun 2020 09:26:59: 3000000 INFO @ Tue, 16 Jun 2020 09:27:00: 9000000 INFO @ Tue, 16 Jun 2020 09:27:04: 4000000 INFO @ Tue, 16 Jun 2020 09:27:05: 10000000 INFO @ Tue, 16 Jun 2020 09:27:10: 5000000 INFO @ Tue, 16 Jun 2020 09:27:10: 11000000 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 09:27:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.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 09:27:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:15: 6000000 INFO @ Tue, 16 Jun 2020 09:27:15: 12000000 INFO @ Tue, 16 Jun 2020 09:27:19: 1000000 INFO @ Tue, 16 Jun 2020 09:27:20: 7000000 INFO @ Tue, 16 Jun 2020 09:27:20: 13000000 INFO @ Tue, 16 Jun 2020 09:27:25: 2000000 INFO @ Tue, 16 Jun 2020 09:27:25: 8000000 INFO @ Tue, 16 Jun 2020 09:27:26: 14000000 INFO @ Tue, 16 Jun 2020 09:27:30: 3000000 INFO @ Tue, 16 Jun 2020 09:27:31: 9000000 INFO @ Tue, 16 Jun 2020 09:27:31: 15000000 INFO @ Tue, 16 Jun 2020 09:27:31: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:27:31: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:27:31: #1 total tags in treatment: 15044506 INFO @ Tue, 16 Jun 2020 09:27:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:31: #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 09:27:32: #1 tags after filtering in treatment: 15044506 INFO @ Tue, 16 Jun 2020 09:27:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:33: #2 number of paired peaks: 421 WARNING @ Tue, 16 Jun 2020 09:27:33: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:33: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:27:33: #2 alternative fragment length(s) may be 2,43 bps INFO @ Tue, 16 Jun 2020 09:27:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.05_model.r WARNING @ Tue, 16 Jun 2020 09:27:33: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:33: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Tue, 16 Jun 2020 09:27:33: #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 09:27:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:35: 4000000 INFO @ Tue, 16 Jun 2020 09:27:36: 10000000 INFO @ Tue, 16 Jun 2020 09:27:41: 5000000 INFO @ Tue, 16 Jun 2020 09:27:41: 11000000 INFO @ Tue, 16 Jun 2020 09:27:46: 6000000 INFO @ Tue, 16 Jun 2020 09:27:46: 12000000 INFO @ Tue, 16 Jun 2020 09:27:51: 7000000 INFO @ Tue, 16 Jun 2020 09:27:51: 13000000 INFO @ Tue, 16 Jun 2020 09:27:57: 14000000 INFO @ Tue, 16 Jun 2020 09:27:57: 8000000 INFO @ Tue, 16 Jun 2020 09:28:02: 15000000 INFO @ Tue, 16 Jun 2020 09:28:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:02: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:28:02: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:28:02: #1 total tags in treatment: 15044506 INFO @ Tue, 16 Jun 2020 09:28:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:02: #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 09:28:02: 9000000 INFO @ Tue, 16 Jun 2020 09:28:02: #1 tags after filtering in treatment: 15044506 INFO @ Tue, 16 Jun 2020 09:28:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:03: #2 number of paired peaks: 421 WARNING @ Tue, 16 Jun 2020 09:28:03: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:04: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:28:04: #2 alternative fragment length(s) may be 2,43 bps INFO @ Tue, 16 Jun 2020 09:28:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.10_model.r WARNING @ Tue, 16 Jun 2020 09:28:04: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:04: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Tue, 16 Jun 2020 09:28:04: #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 09:28:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:07: 10000000 INFO @ Tue, 16 Jun 2020 09:28:12: 11000000 INFO @ Tue, 16 Jun 2020 09:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.05_summits.bed INFO @ Tue, 16 Jun 2020 09:28:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3726 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:18: 12000000 INFO @ Tue, 16 Jun 2020 09:28:23: 13000000 INFO @ Tue, 16 Jun 2020 09:28:28: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:28:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:33: 15000000 INFO @ Tue, 16 Jun 2020 09:28:33: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:28:33: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:28:33: #1 total tags in treatment: 15044506 INFO @ Tue, 16 Jun 2020 09:28:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:33: #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 09:28:33: #1 tags after filtering in treatment: 15044506 INFO @ Tue, 16 Jun 2020 09:28:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:35: #2 number of paired peaks: 421 WARNING @ Tue, 16 Jun 2020 09:28:35: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:35: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 09:28:35: #2 alternative fragment length(s) may be 2,43 bps INFO @ Tue, 16 Jun 2020 09:28:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.20_model.r WARNING @ Tue, 16 Jun 2020 09:28:35: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:35: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Tue, 16 Jun 2020 09:28:35: #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 09:28:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.10_summits.bed INFO @ Tue, 16 Jun 2020 09:28:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (886 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466586/SRX466586.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (241 records, 4 fields): 2 millis CompletedMACS2peakCalling