Job ID = 6455948 SRX = SRX3068984 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:38:14 prefetch.2.10.7: 1) Downloading 'SRR5907460'... 2020-06-21T10:38:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:57 prefetch.2.10.7: 1) 'SRR5907460' was downloaded successfully Read 19008283 spots for SRR5907460/SRR5907460.sra Written 19008283 spots for SRR5907460/SRR5907460.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: 00:04:33 19008283 reads; of these: 19008283 (100.00%) were unpaired; of these: 1702587 (8.96%) aligned 0 times 13889463 (73.07%) aligned exactly 1 time 3416233 (17.97%) aligned >1 times 91.04% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3947150 / 17305696 = 0.2281 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 @ Sun, 21 Jun 2020 19:51:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.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 @ Sun, 21 Jun 2020 19:51:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:59: 1000000 INFO @ Sun, 21 Jun 2020 19:52:04: 2000000 INFO @ Sun, 21 Jun 2020 19:52:10: 3000000 INFO @ Sun, 21 Jun 2020 19:52:15: 4000000 INFO @ Sun, 21 Jun 2020 19:52:21: 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 @ Sun, 21 Jun 2020 19:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.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 @ Sun, 21 Jun 2020 19:52:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:27: 6000000 INFO @ Sun, 21 Jun 2020 19:52:30: 1000000 INFO @ Sun, 21 Jun 2020 19:52:34: 7000000 INFO @ Sun, 21 Jun 2020 19:52:38: 2000000 INFO @ Sun, 21 Jun 2020 19:52:40: 8000000 INFO @ Sun, 21 Jun 2020 19:52:45: 3000000 INFO @ Sun, 21 Jun 2020 19:52:47: 9000000 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 @ Sun, 21 Jun 2020 19:52:52: 4000000 INFO @ Sun, 21 Jun 2020 19:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.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 @ Sun, 21 Jun 2020 19:52:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:53: 10000000 INFO @ Sun, 21 Jun 2020 19:53:00: 5000000 INFO @ Sun, 21 Jun 2020 19:53:00: 1000000 INFO @ Sun, 21 Jun 2020 19:53:00: 11000000 INFO @ Sun, 21 Jun 2020 19:53:07: 2000000 INFO @ Sun, 21 Jun 2020 19:53:07: 6000000 INFO @ Sun, 21 Jun 2020 19:53:07: 12000000 INFO @ Sun, 21 Jun 2020 19:53:14: 3000000 INFO @ Sun, 21 Jun 2020 19:53:14: 13000000 INFO @ Sun, 21 Jun 2020 19:53:14: 7000000 INFO @ Sun, 21 Jun 2020 19:53:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:53:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:53:16: #1 total tags in treatment: 13358546 INFO @ Sun, 21 Jun 2020 19:53:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:53:17: #1 tags after filtering in treatment: 13358546 INFO @ Sun, 21 Jun 2020 19:53:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:17: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:18: #2 number of paired peaks: 451 WARNING @ Sun, 21 Jun 2020 19:53:18: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sun, 21 Jun 2020 19:53:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:18: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:53:18: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sun, 21 Jun 2020 19:53:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.05_model.r WARNING @ Sun, 21 Jun 2020 19:53:18: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:53:18: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sun, 21 Jun 2020 19:53:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:53:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:20: 4000000 INFO @ Sun, 21 Jun 2020 19:53:22: 8000000 INFO @ Sun, 21 Jun 2020 19:53:27: 5000000 INFO @ Sun, 21 Jun 2020 19:53:29: 9000000 INFO @ Sun, 21 Jun 2020 19:53:33: 6000000 INFO @ Sun, 21 Jun 2020 19:53:36: 10000000 INFO @ Sun, 21 Jun 2020 19:53:40: 7000000 INFO @ Sun, 21 Jun 2020 19:53:44: 11000000 INFO @ Sun, 21 Jun 2020 19:53:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:47: 8000000 INFO @ Sun, 21 Jun 2020 19:53:52: 12000000 INFO @ Sun, 21 Jun 2020 19:53:53: 9000000 INFO @ Sun, 21 Jun 2020 19:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.05_summits.bed INFO @ Sun, 21 Jun 2020 19:53:57: Done! pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (2009 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:53:59: 13000000 INFO @ Sun, 21 Jun 2020 19:54:00: 10000000 INFO @ Sun, 21 Jun 2020 19:54:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:54:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:54:02: #1 total tags in treatment: 13358546 INFO @ Sun, 21 Jun 2020 19:54:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:54:03: #1 tags after filtering in treatment: 13358546 INFO @ Sun, 21 Jun 2020 19:54:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:04: #2 number of paired peaks: 451 WARNING @ Sun, 21 Jun 2020 19:54:04: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sun, 21 Jun 2020 19:54:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:04: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:54:04: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sun, 21 Jun 2020 19:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.10_model.r WARNING @ Sun, 21 Jun 2020 19:54:04: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:04: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sun, 21 Jun 2020 19:54:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:54:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:54:06: 11000000 INFO @ Sun, 21 Jun 2020 19:54:12: 12000000 INFO @ Sun, 21 Jun 2020 19:54:18: 13000000 INFO @ Sun, 21 Jun 2020 19:54:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:54:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:54:20: #1 total tags in treatment: 13358546 INFO @ Sun, 21 Jun 2020 19:54:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:54:21: #1 tags after filtering in treatment: 13358546 INFO @ Sun, 21 Jun 2020 19:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:21: #2 number of paired peaks: 451 WARNING @ Sun, 21 Jun 2020 19:54:21: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Sun, 21 Jun 2020 19:54:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:22: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:54:22: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sun, 21 Jun 2020 19:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.20_model.r WARNING @ Sun, 21 Jun 2020 19:54:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:22: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sun, 21 Jun 2020 19:54:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:54:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:54:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.10_summits.bed INFO @ Sun, 21 Jun 2020 19:54:44: Done! pass1 - making usageList (443 chroms): 1 millis pass2 - checking and writing primary data (1555 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:54:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068984/SRX3068984.20_summits.bed INFO @ Sun, 21 Jun 2020 19:54:59: Done! pass1 - making usageList (232 chroms): 1 millis pass2 - checking and writing primary data (435 records, 4 fields): 7 millis CompletedMACS2peakCalling