Job ID = 6498296 SRX = SRX467107 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:29:32 prefetch.2.10.7: 1) Downloading 'SRR1164531'... 2020-06-25T23:29:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:32:15 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:32:16 prefetch.2.10.7: 'SRR1164531' is valid 2020-06-25T23:32:16 prefetch.2.10.7: 1) 'SRR1164531' was downloaded successfully Read 14811631 spots for SRR1164531/SRR1164531.sra Written 14811631 spots for SRR1164531/SRR1164531.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: 00:04:23 14811631 reads; of these: 14811631 (100.00%) were unpaired; of these: 1094624 (7.39%) aligned 0 times 10685156 (72.14%) aligned exactly 1 time 3031851 (20.47%) aligned >1 times 92.61% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1391421 / 13717007 = 0.1014 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 @ Fri, 26 Jun 2020 08:41:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 26 Jun 2020 08:41:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:41:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:41:13: 1000000 INFO @ Fri, 26 Jun 2020 08:41:18: 2000000 INFO @ Fri, 26 Jun 2020 08:41:23: 3000000 INFO @ Fri, 26 Jun 2020 08:41:28: 4000000 INFO @ Fri, 26 Jun 2020 08:41:33: 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 @ Fri, 26 Jun 2020 08:41:38: 6000000 INFO @ Fri, 26 Jun 2020 08:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 26 Jun 2020 08:41:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:41:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:41:43: 7000000 INFO @ Fri, 26 Jun 2020 08:41:43: 1000000 INFO @ Fri, 26 Jun 2020 08:41:48: 8000000 INFO @ Fri, 26 Jun 2020 08:41:48: 2000000 INFO @ Fri, 26 Jun 2020 08:41:53: 9000000 INFO @ Fri, 26 Jun 2020 08:41:53: 3000000 INFO @ Fri, 26 Jun 2020 08:41:58: 10000000 INFO @ Fri, 26 Jun 2020 08:41:58: 4000000 INFO @ Fri, 26 Jun 2020 08:42:03: 11000000 INFO @ Fri, 26 Jun 2020 08:42:03: 5000000 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 @ Fri, 26 Jun 2020 08:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 26 Jun 2020 08:42:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:42:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:42:08: 12000000 INFO @ Fri, 26 Jun 2020 08:42:08: 6000000 INFO @ Fri, 26 Jun 2020 08:42:09: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:42:09: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:42:09: #1 total tags in treatment: 12325586 INFO @ Fri, 26 Jun 2020 08:42:09: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:42:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:42:10: #1 tags after filtering in treatment: 12325586 INFO @ Fri, 26 Jun 2020 08:42:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:42:10: #1 finished! INFO @ Fri, 26 Jun 2020 08:42:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:42:10: #2 number of paired peaks: 153 WARNING @ Fri, 26 Jun 2020 08:42:10: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 26 Jun 2020 08:42:10: start model_add_line... INFO @ Fri, 26 Jun 2020 08:42:10: start X-correlation... INFO @ Fri, 26 Jun 2020 08:42:10: end of X-cor INFO @ Fri, 26 Jun 2020 08:42:10: #2 finished! INFO @ Fri, 26 Jun 2020 08:42:10: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 08:42:10: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 26 Jun 2020 08:42:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.05_model.r WARNING @ Fri, 26 Jun 2020 08:42:11: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:42:11: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 26 Jun 2020 08:42:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:42:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:42:13: 1000000 INFO @ Fri, 26 Jun 2020 08:42:14: 7000000 INFO @ Fri, 26 Jun 2020 08:42:18: 2000000 INFO @ Fri, 26 Jun 2020 08:42:19: 8000000 INFO @ Fri, 26 Jun 2020 08:42:24: 9000000 INFO @ Fri, 26 Jun 2020 08:42:24: 3000000 INFO @ Fri, 26 Jun 2020 08:42:29: 10000000 INFO @ Fri, 26 Jun 2020 08:42:29: 4000000 INFO @ Fri, 26 Jun 2020 08:42:34: 11000000 INFO @ Fri, 26 Jun 2020 08:42:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:42:35: 5000000 INFO @ Fri, 26 Jun 2020 08:42:39: 12000000 INFO @ Fri, 26 Jun 2020 08:42:40: 6000000 INFO @ Fri, 26 Jun 2020 08:42:41: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:42:41: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:42:41: #1 total tags in treatment: 12325586 INFO @ Fri, 26 Jun 2020 08:42:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:42:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:42:41: #1 tags after filtering in treatment: 12325586 INFO @ Fri, 26 Jun 2020 08:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:42:41: #1 finished! INFO @ Fri, 26 Jun 2020 08:42:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:42:42: #2 number of paired peaks: 153 WARNING @ Fri, 26 Jun 2020 08:42:42: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 26 Jun 2020 08:42:42: start model_add_line... INFO @ Fri, 26 Jun 2020 08:42:42: start X-correlation... INFO @ Fri, 26 Jun 2020 08:42:42: end of X-cor INFO @ Fri, 26 Jun 2020 08:42:42: #2 finished! INFO @ Fri, 26 Jun 2020 08:42:42: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 08:42:42: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 26 Jun 2020 08:42:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.10_model.r WARNING @ Fri, 26 Jun 2020 08:42:42: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:42:42: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 26 Jun 2020 08:42:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:42:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:42:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:42:45: 7000000 INFO @ Fri, 26 Jun 2020 08:42:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:42:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:42:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.05_summits.bed INFO @ Fri, 26 Jun 2020 08:42:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1569 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:42:50: 8000000 INFO @ Fri, 26 Jun 2020 08:42:55: 9000000 INFO @ Fri, 26 Jun 2020 08:43:00: 10000000 INFO @ Fri, 26 Jun 2020 08:43:05: 11000000 INFO @ Fri, 26 Jun 2020 08:43:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:43:10: 12000000 INFO @ Fri, 26 Jun 2020 08:43:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:43:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:43:12: #1 total tags in treatment: 12325586 INFO @ Fri, 26 Jun 2020 08:43:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:43:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:43:12: #1 tags after filtering in treatment: 12325586 INFO @ Fri, 26 Jun 2020 08:43:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:43:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:43:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:43:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:43:13: #2 number of paired peaks: 153 WARNING @ Fri, 26 Jun 2020 08:43:13: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 26 Jun 2020 08:43:13: start model_add_line... INFO @ Fri, 26 Jun 2020 08:43:13: start X-correlation... INFO @ Fri, 26 Jun 2020 08:43:13: end of X-cor INFO @ Fri, 26 Jun 2020 08:43:13: #2 finished! INFO @ Fri, 26 Jun 2020 08:43:13: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 08:43:13: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 26 Jun 2020 08:43:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.20_model.r WARNING @ Fri, 26 Jun 2020 08:43:13: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:43:13: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 26 Jun 2020 08:43:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:43:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:43:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.10_summits.bed INFO @ Fri, 26 Jun 2020 08:43:18: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1292 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:43:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:43:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:43:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:43:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467107/SRX467107.20_summits.bed INFO @ Fri, 26 Jun 2020 08:43:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (895 records, 4 fields): 3 millis CompletedMACS2peakCalling