Job ID = 6366988 SRX = SRX257687 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:46 prefetch.2.10.7: 1) Downloading 'SRR800703'... 2020-06-15T23:09:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:29 prefetch.2.10.7: 1) 'SRR800703' was downloaded successfully Read 17156712 spots for SRR800703/SRR800703.sra Written 17156712 spots for SRR800703/SRR800703.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: 00:03:45 17156712 reads; of these: 17156712 (100.00%) were unpaired; of these: 639930 (3.73%) aligned 0 times 13660081 (79.62%) aligned exactly 1 time 2856701 (16.65%) aligned >1 times 96.27% overall alignment rate Time searching: 00:03:45 Overall time: 00:03:45 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] 5340662 / 16516782 = 0.3233 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 08:21:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.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 08:21:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:18: 1000000 INFO @ Tue, 16 Jun 2020 08:21:25: 2000000 INFO @ Tue, 16 Jun 2020 08:21:31: 3000000 INFO @ Tue, 16 Jun 2020 08:21:38: 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 08:21:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.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 08:21:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:45: 5000000 INFO @ Tue, 16 Jun 2020 08:21:48: 1000000 INFO @ Tue, 16 Jun 2020 08:21:53: 6000000 INFO @ Tue, 16 Jun 2020 08:21:55: 2000000 INFO @ Tue, 16 Jun 2020 08:22:00: 7000000 INFO @ Tue, 16 Jun 2020 08:22:02: 3000000 INFO @ Tue, 16 Jun 2020 08:22:08: 8000000 INFO @ Tue, 16 Jun 2020 08:22:09: 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 08:22:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.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 08:22:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:22:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:22:15: 9000000 INFO @ Tue, 16 Jun 2020 08:22:15: 5000000 INFO @ Tue, 16 Jun 2020 08:22:18: 1000000 INFO @ Tue, 16 Jun 2020 08:22:22: 6000000 INFO @ Tue, 16 Jun 2020 08:22:23: 10000000 INFO @ Tue, 16 Jun 2020 08:22:25: 2000000 INFO @ Tue, 16 Jun 2020 08:22:29: 7000000 INFO @ Tue, 16 Jun 2020 08:22:30: 11000000 INFO @ Tue, 16 Jun 2020 08:22:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:22:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:22:32: #1 total tags in treatment: 11176120 INFO @ Tue, 16 Jun 2020 08:22:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:32: #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 08:22:32: #1 tags after filtering in treatment: 11176120 INFO @ Tue, 16 Jun 2020 08:22:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:32: 3000000 INFO @ Tue, 16 Jun 2020 08:22:33: #2 number of paired peaks: 401 WARNING @ Tue, 16 Jun 2020 08:22:33: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:33: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:22:33: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 08:22:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.05_model.r WARNING @ Tue, 16 Jun 2020 08:22:33: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:33: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 08:22:33: #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 08:22:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:36: 8000000 INFO @ Tue, 16 Jun 2020 08:22:39: 4000000 INFO @ Tue, 16 Jun 2020 08:22:43: 9000000 INFO @ Tue, 16 Jun 2020 08:22:46: 5000000 INFO @ Tue, 16 Jun 2020 08:22:50: 10000000 INFO @ Tue, 16 Jun 2020 08:22:52: 6000000 INFO @ Tue, 16 Jun 2020 08:22:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:56: 11000000 INFO @ Tue, 16 Jun 2020 08:22:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:22:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:22:57: #1 total tags in treatment: 11176120 INFO @ Tue, 16 Jun 2020 08:22:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:57: #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 08:22:58: #1 tags after filtering in treatment: 11176120 INFO @ Tue, 16 Jun 2020 08:22:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:58: #2 number of paired peaks: 401 WARNING @ Tue, 16 Jun 2020 08:22:58: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:58: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:22:58: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 08:22:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.10_model.r WARNING @ Tue, 16 Jun 2020 08:22:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:58: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 08:22:58: #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 08:22:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:59: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:23:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.05_summits.bed INFO @ Tue, 16 Jun 2020 08:23:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (900 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:05: 8000000 INFO @ Tue, 16 Jun 2020 08:23:11: 9000000 INFO @ Tue, 16 Jun 2020 08:23:16: 10000000 INFO @ Tue, 16 Jun 2020 08:23:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:22: 11000000 INFO @ Tue, 16 Jun 2020 08:23:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:23:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:23:23: #1 total tags in treatment: 11176120 INFO @ Tue, 16 Jun 2020 08:23:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:23:23: #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 08:23:23: #1 tags after filtering in treatment: 11176120 INFO @ Tue, 16 Jun 2020 08:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:23:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:23:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:23:24: #2 number of paired peaks: 401 WARNING @ Tue, 16 Jun 2020 08:23:24: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Tue, 16 Jun 2020 08:23:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:23:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:23:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:23:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:23:24: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:23:24: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 08:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.20_model.r WARNING @ Tue, 16 Jun 2020 08:23:24: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:23:24: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 08:23:24: #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 08:23:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:23:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:23:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.10_summits.bed INFO @ Tue, 16 Jun 2020 08:23:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (563 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257687/SRX257687.20_summits.bed INFO @ Tue, 16 Jun 2020 08:23:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (206 records, 4 fields): 1 millis CompletedMACS2peakCalling