Job ID = 6366743 SRX = SRX2228896 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:53 prefetch.2.10.7: 1) Downloading 'SRR4380352'... 2020-06-15T23:07:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:09:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:09:23 prefetch.2.10.7: 'SRR4380352' is valid 2020-06-15T23:09:23 prefetch.2.10.7: 1) 'SRR4380352' was downloaded successfully Read 15226514 spots for SRR4380352/SRR4380352.sra Written 15226514 spots for SRR4380352/SRR4380352.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:39 15226514 reads; of these: 15226514 (100.00%) were unpaired; of these: 98729 (0.65%) aligned 0 times 12677895 (83.26%) aligned exactly 1 time 2449890 (16.09%) aligned >1 times 99.35% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 1348307 / 15127785 = 0.0891 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 08:18:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.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 08:18:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:26: 1000000 INFO @ Tue, 16 Jun 2020 08:18:32: 2000000 INFO @ Tue, 16 Jun 2020 08:18:38: 3000000 INFO @ Tue, 16 Jun 2020 08:18:43: 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 08:18:49: 5000000 INFO @ Tue, 16 Jun 2020 08:18:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.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 08:18:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:54: 6000000 INFO @ Tue, 16 Jun 2020 08:18:57: 1000000 INFO @ Tue, 16 Jun 2020 08:19:00: 7000000 INFO @ Tue, 16 Jun 2020 08:19:03: 2000000 INFO @ Tue, 16 Jun 2020 08:19:06: 8000000 INFO @ Tue, 16 Jun 2020 08:19:09: 3000000 INFO @ Tue, 16 Jun 2020 08:19:12: 9000000 INFO @ Tue, 16 Jun 2020 08:19:15: 4000000 INFO @ Tue, 16 Jun 2020 08:19:18: 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 08:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.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 08:19:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:21: 5000000 INFO @ Tue, 16 Jun 2020 08:19:24: 11000000 INFO @ Tue, 16 Jun 2020 08:19:27: 6000000 INFO @ Tue, 16 Jun 2020 08:19:27: 1000000 INFO @ Tue, 16 Jun 2020 08:19:30: 12000000 INFO @ Tue, 16 Jun 2020 08:19:33: 7000000 INFO @ Tue, 16 Jun 2020 08:19:34: 2000000 INFO @ Tue, 16 Jun 2020 08:19:36: 13000000 INFO @ Tue, 16 Jun 2020 08:19:39: 8000000 INFO @ Tue, 16 Jun 2020 08:19:40: 3000000 INFO @ Tue, 16 Jun 2020 08:19:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:19:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:19:40: #1 total tags in treatment: 13779478 INFO @ Tue, 16 Jun 2020 08:19:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:40: #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 08:19:41: #1 tags after filtering in treatment: 13779478 INFO @ Tue, 16 Jun 2020 08:19:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:42: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:19:42: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:42: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:19:42: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.05_model.r WARNING @ Tue, 16 Jun 2020 08:19:42: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:42: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:19:42: #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 08:19:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:44: 9000000 INFO @ Tue, 16 Jun 2020 08:19:47: 4000000 INFO @ Tue, 16 Jun 2020 08:19:50: 10000000 INFO @ Tue, 16 Jun 2020 08:19:53: 5000000 INFO @ Tue, 16 Jun 2020 08:19:57: 11000000 INFO @ Tue, 16 Jun 2020 08:20:00: 6000000 INFO @ Tue, 16 Jun 2020 08:20:03: 12000000 INFO @ Tue, 16 Jun 2020 08:20:07: 7000000 INFO @ Tue, 16 Jun 2020 08:20:09: 13000000 INFO @ Tue, 16 Jun 2020 08:20:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:13: 8000000 INFO @ Tue, 16 Jun 2020 08:20:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:14: #1 total tags in treatment: 13779478 INFO @ Tue, 16 Jun 2020 08:20:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:14: #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 08:20:14: #1 tags after filtering in treatment: 13779478 INFO @ Tue, 16 Jun 2020 08:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:15: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:20:15: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:15: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:20:15: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.10_model.r WARNING @ Tue, 16 Jun 2020 08:20:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:15: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:20:15: #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 08:20:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:20: 9000000 INFO @ Tue, 16 Jun 2020 08:20:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (600 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:27: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:33: 11000000 INFO @ Tue, 16 Jun 2020 08:20:40: 12000000 INFO @ Tue, 16 Jun 2020 08:20:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:47: 13000000 INFO @ Tue, 16 Jun 2020 08:20:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:53: #1 total tags in treatment: 13779478 INFO @ Tue, 16 Jun 2020 08:20:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:53: #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 08:20:53: #1 tags after filtering in treatment: 13779478 INFO @ Tue, 16 Jun 2020 08:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:54: #2 number of paired peaks: 225 WARNING @ Tue, 16 Jun 2020 08:20:54: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:54: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:20:54: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.20_model.r WARNING @ Tue, 16 Jun 2020 08:20:54: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:54: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:20:54: #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 08:20:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (343 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228896/SRX2228896.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 1 millis CompletedMACS2peakCalling