Job ID = 6455469 SRX = SRX287814 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:24:21 prefetch.2.10.7: 1) Downloading 'SRR870003'... 2020-06-21T10:24:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:04 prefetch.2.10.7: 1) 'SRR870003' was downloaded successfully Read 17667108 spots for SRR870003/SRR870003.sra Written 17667108 spots for SRR870003/SRR870003.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: 00:05:51 17667108 reads; of these: 17667108 (100.00%) were unpaired; of these: 989045 (5.60%) aligned 0 times 11539920 (65.32%) aligned exactly 1 time 5138143 (29.08%) aligned >1 times 94.40% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 2391693 / 16678063 = 0.1434 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 19:39:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.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 19:39:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:36: 1000000 INFO @ Sun, 21 Jun 2020 19:39:44: 2000000 INFO @ Sun, 21 Jun 2020 19:39:51: 3000000 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 19:39:59: 4000000 INFO @ Sun, 21 Jun 2020 19:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.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 19:39:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:07: 5000000 INFO @ Sun, 21 Jun 2020 19:40:07: 1000000 INFO @ Sun, 21 Jun 2020 19:40:15: 6000000 INFO @ Sun, 21 Jun 2020 19:40:15: 2000000 INFO @ Sun, 21 Jun 2020 19:40:23: 7000000 INFO @ Sun, 21 Jun 2020 19:40:24: 3000000 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 19:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.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 19:40:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:40:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:31: 8000000 INFO @ Sun, 21 Jun 2020 19:40:32: 4000000 INFO @ Sun, 21 Jun 2020 19:40:38: 1000000 INFO @ Sun, 21 Jun 2020 19:40:39: 9000000 INFO @ Sun, 21 Jun 2020 19:40:40: 5000000 INFO @ Sun, 21 Jun 2020 19:40:46: 2000000 INFO @ Sun, 21 Jun 2020 19:40:47: 10000000 INFO @ Sun, 21 Jun 2020 19:40:49: 6000000 INFO @ Sun, 21 Jun 2020 19:40:54: 3000000 INFO @ Sun, 21 Jun 2020 19:40:56: 11000000 INFO @ Sun, 21 Jun 2020 19:40:57: 7000000 INFO @ Sun, 21 Jun 2020 19:41:02: 4000000 INFO @ Sun, 21 Jun 2020 19:41:05: 12000000 INFO @ Sun, 21 Jun 2020 19:41:05: 8000000 INFO @ Sun, 21 Jun 2020 19:41:11: 5000000 INFO @ Sun, 21 Jun 2020 19:41:13: 13000000 INFO @ Sun, 21 Jun 2020 19:41:14: 9000000 INFO @ Sun, 21 Jun 2020 19:41:19: 6000000 INFO @ Sun, 21 Jun 2020 19:41:22: 14000000 INFO @ Sun, 21 Jun 2020 19:41:22: 10000000 INFO @ Sun, 21 Jun 2020 19:41:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:41:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:41:24: #1 total tags in treatment: 14286370 INFO @ Sun, 21 Jun 2020 19:41:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:24: #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 19:41:25: #1 tags after filtering in treatment: 14286370 INFO @ Sun, 21 Jun 2020 19:41:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:26: #2 number of paired peaks: 443 WARNING @ Sun, 21 Jun 2020 19:41:26: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sun, 21 Jun 2020 19:41:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:26: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:41:26: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.05_model.r WARNING @ Sun, 21 Jun 2020 19:41:26: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:41:26: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:41:26: #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 19:41:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:41:28: 7000000 INFO @ Sun, 21 Jun 2020 19:41:30: 11000000 INFO @ Sun, 21 Jun 2020 19:41:36: 8000000 INFO @ Sun, 21 Jun 2020 19:41:39: 12000000 INFO @ Sun, 21 Jun 2020 19:41:43: 9000000 INFO @ Sun, 21 Jun 2020 19:41:47: 13000000 INFO @ Sun, 21 Jun 2020 19:41:51: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:41:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:56: 14000000 INFO @ Sun, 21 Jun 2020 19:41:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:41:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:41:58: #1 total tags in treatment: 14286370 INFO @ Sun, 21 Jun 2020 19:41:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:58: #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 19:41:59: #1 tags after filtering in treatment: 14286370 INFO @ Sun, 21 Jun 2020 19:41:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:59: 11000000 INFO @ Sun, 21 Jun 2020 19:42:00: #2 number of paired peaks: 443 WARNING @ Sun, 21 Jun 2020 19:42:00: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sun, 21 Jun 2020 19:42:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:00: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:42:00: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:42:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.10_model.r WARNING @ Sun, 21 Jun 2020 19:42:00: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:42:00: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:42:00: #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 19:42:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.05_summits.bed INFO @ Sun, 21 Jun 2020 19:42:05: Done! pass1 - making usageList (608 chroms): 2 millis pass2 - checking and writing primary data (2331 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:42:07: 12000000 INFO @ Sun, 21 Jun 2020 19:42:15: 13000000 INFO @ Sun, 21 Jun 2020 19:42:22: 14000000 INFO @ Sun, 21 Jun 2020 19:42:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:42:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:42:25: #1 total tags in treatment: 14286370 INFO @ Sun, 21 Jun 2020 19:42:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:25: #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 19:42:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:42:25: #1 tags after filtering in treatment: 14286370 INFO @ Sun, 21 Jun 2020 19:42:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:26: #2 number of paired peaks: 443 WARNING @ Sun, 21 Jun 2020 19:42:26: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sun, 21 Jun 2020 19:42:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:26: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:42:26: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.20_model.r WARNING @ Sun, 21 Jun 2020 19:42:26: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:42:26: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:42:26: #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 19:42:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:42:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:42:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.10_summits.bed INFO @ Sun, 21 Jun 2020 19:42:38: Done! pass1 - making usageList (510 chroms): 2 millis pass2 - checking and writing primary data (1832 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:42:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287814/SRX287814.20_summits.bed INFO @ Sun, 21 Jun 2020 19:43:05: Done! pass1 - making usageList (312 chroms): 1 millis pass2 - checking and writing primary data (648 records, 4 fields): 18 millis CompletedMACS2peakCalling