Job ID = 6366970 SRX = SRX257669 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:24:20 prefetch.2.10.7: 1) Downloading 'SRR800680'... 2020-06-15T23:24:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:25:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:25:20 prefetch.2.10.7: 'SRR800680' is valid 2020-06-15T23:25:20 prefetch.2.10.7: 1) 'SRR800680' was downloaded successfully Read 12641662 spots for SRR800680/SRR800680.sra Written 12641662 spots for SRR800680/SRR800680.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: 00:03:04 12641662 reads; of these: 12641662 (100.00%) were unpaired; of these: 633675 (5.01%) aligned 0 times 9922198 (78.49%) aligned exactly 1 time 2085789 (16.50%) aligned >1 times 94.99% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 1066900 / 12007987 = 0.0888 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 08:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.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 08:33:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:32: 1000000 INFO @ Tue, 16 Jun 2020 08:33:38: 2000000 INFO @ Tue, 16 Jun 2020 08:33:44: 3000000 INFO @ Tue, 16 Jun 2020 08:33:50: 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 08:33:56: 5000000 INFO @ Tue, 16 Jun 2020 08:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.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 08:33:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:02: 6000000 INFO @ Tue, 16 Jun 2020 08:34:02: 1000000 INFO @ Tue, 16 Jun 2020 08:34:08: 7000000 INFO @ Tue, 16 Jun 2020 08:34:09: 2000000 INFO @ Tue, 16 Jun 2020 08:34:14: 8000000 INFO @ Tue, 16 Jun 2020 08:34:15: 3000000 INFO @ Tue, 16 Jun 2020 08:34:20: 9000000 INFO @ Tue, 16 Jun 2020 08:34:22: 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 08:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.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 08:34:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:27: 10000000 INFO @ Tue, 16 Jun 2020 08:34:29: 5000000 INFO @ Tue, 16 Jun 2020 08:34:33: 1000000 INFO @ Tue, 16 Jun 2020 08:34:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:34:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:34:33: #1 total tags in treatment: 10941087 INFO @ Tue, 16 Jun 2020 08:34:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:33: #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 08:34:34: #1 tags after filtering in treatment: 10941087 INFO @ Tue, 16 Jun 2020 08:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:34: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 08:34:34: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 08:34:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:35: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:34:35: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.05_model.r WARNING @ Tue, 16 Jun 2020 08:34:35: #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 08:34:35: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:34:35: #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 08:34:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:34:35: 6000000 INFO @ Tue, 16 Jun 2020 08:34:40: 2000000 INFO @ Tue, 16 Jun 2020 08:34:42: 7000000 INFO @ Tue, 16 Jun 2020 08:34:47: 3000000 INFO @ Tue, 16 Jun 2020 08:34:48: 8000000 INFO @ Tue, 16 Jun 2020 08:34:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:54: 4000000 INFO @ Tue, 16 Jun 2020 08:34:54: 9000000 INFO @ Tue, 16 Jun 2020 08:35:00: 5000000 INFO @ Tue, 16 Jun 2020 08:35:01: 10000000 INFO @ Tue, 16 Jun 2020 08:35:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.05_summits.bed INFO @ Tue, 16 Jun 2020 08:35:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (651 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:06: 6000000 INFO @ Tue, 16 Jun 2020 08:35:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:35:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:35:07: #1 total tags in treatment: 10941087 INFO @ Tue, 16 Jun 2020 08:35:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:07: #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 08:35:07: #1 tags after filtering in treatment: 10941087 INFO @ Tue, 16 Jun 2020 08:35:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:08: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 08:35:08: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:08: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:35:08: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.10_model.r WARNING @ Tue, 16 Jun 2020 08:35:08: #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 08:35:08: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:35:08: #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 08:35:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:12: 7000000 INFO @ Tue, 16 Jun 2020 08:35:19: 8000000 INFO @ Tue, 16 Jun 2020 08:35:26: 9000000 INFO @ Tue, 16 Jun 2020 08:35:27: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:32: 10000000 INFO @ Tue, 16 Jun 2020 08:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.10_summits.bed INFO @ Tue, 16 Jun 2020 08:35:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:35:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:35:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:35:37: #1 total tags in treatment: 10941087 INFO @ Tue, 16 Jun 2020 08:35:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:37: #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 08:35:38: #1 tags after filtering in treatment: 10941087 INFO @ Tue, 16 Jun 2020 08:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:38: #2 number of paired peaks: 313 WARNING @ Tue, 16 Jun 2020 08:35:38: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:38: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:35:38: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:35:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.20_model.r WARNING @ Tue, 16 Jun 2020 08:35:38: #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 08:35:38: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:35:38: #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 08:35:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:36:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257669/SRX257669.20_summits.bed INFO @ Tue, 16 Jun 2020 08:36:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling