Job ID = 6455618 SRX = SRX287931 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:12:52 prefetch.2.10.7: 1) Downloading 'SRR870120'... 2020-06-21T10:12:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:15:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:15:20 prefetch.2.10.7: 1) 'SRR870120' was downloaded successfully Read 17355751 spots for SRR870120/SRR870120.sra Written 17355751 spots for SRR870120/SRR870120.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: 00:05:15 17355751 reads; of these: 17355751 (100.00%) were unpaired; of these: 1248878 (7.20%) aligned 0 times 10894768 (62.77%) aligned exactly 1 time 5212105 (30.03%) aligned >1 times 92.80% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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] 3083999 / 16106873 = 0.1915 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 19:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.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 19:25:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:42: 1000000 INFO @ Sun, 21 Jun 2020 19:25:47: 2000000 INFO @ Sun, 21 Jun 2020 19:25:52: 3000000 INFO @ Sun, 21 Jun 2020 19:25:58: 4000000 INFO @ Sun, 21 Jun 2020 19:26:03: 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 19:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.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 19:26:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:08: 6000000 INFO @ Sun, 21 Jun 2020 19:26:13: 1000000 INFO @ Sun, 21 Jun 2020 19:26:14: 7000000 INFO @ Sun, 21 Jun 2020 19:26:19: 2000000 INFO @ Sun, 21 Jun 2020 19:26:19: 8000000 INFO @ Sun, 21 Jun 2020 19:26:24: 9000000 INFO @ Sun, 21 Jun 2020 19:26:24: 3000000 INFO @ Sun, 21 Jun 2020 19:26:29: 10000000 INFO @ Sun, 21 Jun 2020 19:26:30: 4000000 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 19:26:35: 11000000 INFO @ Sun, 21 Jun 2020 19:26:36: 5000000 INFO @ Sun, 21 Jun 2020 19:26:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.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 19:26:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:41: 12000000 INFO @ Sun, 21 Jun 2020 19:26:42: 6000000 INFO @ Sun, 21 Jun 2020 19:26:43: 1000000 INFO @ Sun, 21 Jun 2020 19:26:46: 13000000 INFO @ Sun, 21 Jun 2020 19:26:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:47: #1 total tags in treatment: 13022874 INFO @ Sun, 21 Jun 2020 19:26:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:47: #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 19:26:47: #1 tags after filtering in treatment: 13022874 INFO @ Sun, 21 Jun 2020 19:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:47: 7000000 INFO @ Sun, 21 Jun 2020 19:26:48: #2 number of paired peaks: 823 WARNING @ Sun, 21 Jun 2020 19:26:48: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sun, 21 Jun 2020 19:26:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:48: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:26:48: #2 alternative fragment length(s) may be 3,38 bps INFO @ Sun, 21 Jun 2020 19:26:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.05_model.r WARNING @ Sun, 21 Jun 2020 19:26:48: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:26:48: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Sun, 21 Jun 2020 19:26:48: #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 19:26:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:49: 2000000 INFO @ Sun, 21 Jun 2020 19:26:53: 8000000 INFO @ Sun, 21 Jun 2020 19:26:55: 3000000 INFO @ Sun, 21 Jun 2020 19:26:59: 9000000 INFO @ Sun, 21 Jun 2020 19:27:01: 4000000 INFO @ Sun, 21 Jun 2020 19:27:05: 10000000 INFO @ Sun, 21 Jun 2020 19:27:06: 5000000 INFO @ Sun, 21 Jun 2020 19:27:11: 11000000 INFO @ Sun, 21 Jun 2020 19:27:12: 6000000 INFO @ Sun, 21 Jun 2020 19:27:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:17: 12000000 INFO @ Sun, 21 Jun 2020 19:27:18: 7000000 INFO @ Sun, 21 Jun 2020 19:27:23: 13000000 INFO @ Sun, 21 Jun 2020 19:27:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:23: #1 total tags in treatment: 13022874 INFO @ Sun, 21 Jun 2020 19:27:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:23: #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 19:27:23: 8000000 INFO @ Sun, 21 Jun 2020 19:27:24: #1 tags after filtering in treatment: 13022874 INFO @ Sun, 21 Jun 2020 19:27:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:24: #2 number of paired peaks: 823 WARNING @ Sun, 21 Jun 2020 19:27:24: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:25: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:27:25: #2 alternative fragment length(s) may be 3,38 bps INFO @ Sun, 21 Jun 2020 19:27:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.10_model.r WARNING @ Sun, 21 Jun 2020 19:27:25: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:25: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Sun, 21 Jun 2020 19:27:25: #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 19:27:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.05_summits.bed INFO @ Sun, 21 Jun 2020 19:27:27: Done! pass1 - making usageList (632 chroms): 1 millis pass2 - checking and writing primary data (2353 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:27:29: 9000000 INFO @ Sun, 21 Jun 2020 19:27:35: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:27:41: 11000000 INFO @ Sun, 21 Jun 2020 19:27:47: 12000000 INFO @ Sun, 21 Jun 2020 19:27:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:52: 13000000 INFO @ Sun, 21 Jun 2020 19:27:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:53: #1 total tags in treatment: 13022874 INFO @ Sun, 21 Jun 2020 19:27:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:53: #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 19:27:53: #1 tags after filtering in treatment: 13022874 INFO @ Sun, 21 Jun 2020 19:27:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:54: #2 number of paired peaks: 823 WARNING @ Sun, 21 Jun 2020 19:27:54: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sun, 21 Jun 2020 19:27:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:54: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 19:27:54: #2 alternative fragment length(s) may be 3,38 bps INFO @ Sun, 21 Jun 2020 19:27:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.20_model.r WARNING @ Sun, 21 Jun 2020 19:27:54: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:27:54: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Sun, 21 Jun 2020 19:27:54: #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 19:27:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.10_summits.bed INFO @ Sun, 21 Jun 2020 19:28:02: Done! pass1 - making usageList (522 chroms): 1 millis pass2 - checking and writing primary data (1994 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:28:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287931/SRX287931.20_summits.bed INFO @ Sun, 21 Jun 2020 19:28:32: Done! pass1 - making usageList (402 chroms): 1 millis pass2 - checking and writing primary data (1051 records, 4 fields): 14 millis CompletedMACS2peakCalling