Job ID = 8069491 SRX = SRX7191476 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-08T03:33:44 prefetch.2.10.7: 1) Downloading 'SRR10502460'... 2020-08-08T03:33:44 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:41 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:42 prefetch.2.10.7: 'SRR10502460' is valid 2020-08-08T03:34:42 prefetch.2.10.7: 1) 'SRR10502460' was downloaded successfully Read 14750486 spots for SRR10502460/SRR10502460.sra Written 14750486 spots for SRR10502460/SRR10502460.sra fastq に変換しました。 bowtie でマッピング中... Your job 8069954 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:24 14750486 reads; of these: 14750486 (100.00%) were unpaired; of these: 388335 (2.63%) aligned 0 times 10035456 (68.03%) aligned exactly 1 time 4326695 (29.33%) aligned >1 times 97.37% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 1215908 / 14362151 = 0.0847 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 @ Sat, 08 Aug 2020 12:44:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.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 @ Sat, 08 Aug 2020 12:44:09: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:44:09: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:44:14: 1000000 INFO @ Sat, 08 Aug 2020 12:44:19: 2000000 INFO @ Sat, 08 Aug 2020 12:44:23: 3000000 INFO @ Sat, 08 Aug 2020 12:44:28: 4000000 INFO @ Sat, 08 Aug 2020 12:44:33: 5000000 INFO @ Sat, 08 Aug 2020 12:44:37: 6000000 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 @ Sat, 08 Aug 2020 12:44:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.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 @ Sat, 08 Aug 2020 12:44:39: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:44:39: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:44:42: 7000000 INFO @ Sat, 08 Aug 2020 12:44:44: 1000000 INFO @ Sat, 08 Aug 2020 12:44:47: 8000000 INFO @ Sat, 08 Aug 2020 12:44:49: 2000000 INFO @ Sat, 08 Aug 2020 12:44:52: 9000000 INFO @ Sat, 08 Aug 2020 12:44:54: 3000000 INFO @ Sat, 08 Aug 2020 12:44:56: 10000000 INFO @ Sat, 08 Aug 2020 12:44:59: 4000000 INFO @ Sat, 08 Aug 2020 12:45:01: 11000000 INFO @ Sat, 08 Aug 2020 12:45:04: 5000000 INFO @ Sat, 08 Aug 2020 12:45:06: 12000000 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 @ Sat, 08 Aug 2020 12:45:08: 6000000 INFO @ Sat, 08 Aug 2020 12:45:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.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 @ Sat, 08 Aug 2020 12:45:09: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:45:09: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:45:11: 13000000 INFO @ Sat, 08 Aug 2020 12:45:12: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:45:12: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:45:12: #1 total tags in treatment: 13146243 INFO @ Sat, 08 Aug 2020 12:45:12: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:45:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:45:12: #1 tags after filtering in treatment: 13146243 INFO @ Sat, 08 Aug 2020 12:45:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:45:12: #1 finished! INFO @ Sat, 08 Aug 2020 12:45:12: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:45:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:45:13: #2 number of paired peaks: 143 WARNING @ Sat, 08 Aug 2020 12:45:13: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 08 Aug 2020 12:45:13: start model_add_line... INFO @ Sat, 08 Aug 2020 12:45:13: start X-correlation... INFO @ Sat, 08 Aug 2020 12:45:13: end of X-cor INFO @ Sat, 08 Aug 2020 12:45:13: #2 finished! INFO @ Sat, 08 Aug 2020 12:45:13: #2 predicted fragment length is 52 bps INFO @ Sat, 08 Aug 2020 12:45:13: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 08 Aug 2020 12:45:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.05_model.r WARNING @ Sat, 08 Aug 2020 12:45:13: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:45:13: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 08 Aug 2020 12:45:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:45:13: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:45:13: 7000000 INFO @ Sat, 08 Aug 2020 12:45:14: 1000000 INFO @ Sat, 08 Aug 2020 12:45:18: 8000000 INFO @ Sat, 08 Aug 2020 12:45:19: 2000000 INFO @ Sat, 08 Aug 2020 12:45:23: 9000000 INFO @ Sat, 08 Aug 2020 12:45:24: 3000000 INFO @ Sat, 08 Aug 2020 12:45:28: 10000000 INFO @ Sat, 08 Aug 2020 12:45:29: 4000000 INFO @ Sat, 08 Aug 2020 12:45:32: 11000000 INFO @ Sat, 08 Aug 2020 12:45:33: 5000000 INFO @ Sat, 08 Aug 2020 12:45:36: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:45:37: 12000000 INFO @ Sat, 08 Aug 2020 12:45:38: 6000000 INFO @ Sat, 08 Aug 2020 12:45:42: 13000000 INFO @ Sat, 08 Aug 2020 12:45:43: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:45:43: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:45:43: #1 total tags in treatment: 13146243 INFO @ Sat, 08 Aug 2020 12:45:43: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:45:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:45:43: 7000000 INFO @ Sat, 08 Aug 2020 12:45:43: #1 tags after filtering in treatment: 13146243 INFO @ Sat, 08 Aug 2020 12:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:45:43: #1 finished! INFO @ Sat, 08 Aug 2020 12:45:43: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:45:44: #2 number of paired peaks: 143 WARNING @ Sat, 08 Aug 2020 12:45:44: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 08 Aug 2020 12:45:44: start model_add_line... INFO @ Sat, 08 Aug 2020 12:45:44: start X-correlation... INFO @ Sat, 08 Aug 2020 12:45:44: end of X-cor INFO @ Sat, 08 Aug 2020 12:45:44: #2 finished! INFO @ Sat, 08 Aug 2020 12:45:44: #2 predicted fragment length is 52 bps INFO @ Sat, 08 Aug 2020 12:45:44: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 08 Aug 2020 12:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.10_model.r WARNING @ Sat, 08 Aug 2020 12:45:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:45:44: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 08 Aug 2020 12:45:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:45:44: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:45:48: 8000000 INFO @ Sat, 08 Aug 2020 12:45:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:45:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:45:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.05_summits.bed INFO @ Sat, 08 Aug 2020 12:45:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2098 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:45:52: 9000000 INFO @ Sat, 08 Aug 2020 12:45:57: 10000000 INFO @ Sat, 08 Aug 2020 12:46:02: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:46:06: 12000000 INFO @ Sat, 08 Aug 2020 12:46:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:46:11: 13000000 INFO @ Sat, 08 Aug 2020 12:46:12: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:46:12: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:46:12: #1 total tags in treatment: 13146243 INFO @ Sat, 08 Aug 2020 12:46:12: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:46:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:46:12: #1 tags after filtering in treatment: 13146243 INFO @ Sat, 08 Aug 2020 12:46:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:46:12: #1 finished! INFO @ Sat, 08 Aug 2020 12:46:12: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:46:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:46:13: #2 number of paired peaks: 143 WARNING @ Sat, 08 Aug 2020 12:46:13: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 08 Aug 2020 12:46:13: start model_add_line... INFO @ Sat, 08 Aug 2020 12:46:13: start X-correlation... INFO @ Sat, 08 Aug 2020 12:46:13: end of X-cor INFO @ Sat, 08 Aug 2020 12:46:13: #2 finished! INFO @ Sat, 08 Aug 2020 12:46:13: #2 predicted fragment length is 52 bps INFO @ Sat, 08 Aug 2020 12:46:13: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 08 Aug 2020 12:46:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.20_model.r WARNING @ Sat, 08 Aug 2020 12:46:13: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:46:13: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 08 Aug 2020 12:46:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:46:13: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:46:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:46:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:46:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:46:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.10_summits.bed INFO @ Sat, 08 Aug 2020 12:46:20: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1406 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:46:37: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:46:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:46:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:46:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191476/SRX7191476.20_summits.bed INFO @ Sat, 08 Aug 2020 12:46:49: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (806 records, 4 fields): 2 millis CompletedMACS2peakCalling