Job ID = 6456114 SRX = SRX318787 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:31:51 prefetch.2.10.7: 1) Downloading 'SRR927103'... 2020-06-21T10:31:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:36:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:36:56 prefetch.2.10.7: 1) 'SRR927103' was downloaded successfully Read 18249589 spots for SRR927103/SRR927103.sra Written 18249589 spots for SRR927103/SRR927103.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: 00:04:58 18249589 reads; of these: 18249589 (100.00%) were unpaired; of these: 1102823 (6.04%) aligned 0 times 13105525 (71.81%) aligned exactly 1 time 4041241 (22.14%) aligned >1 times 93.96% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 2105774 / 17146766 = 0.1228 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 19:47:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.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 19:47:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:33: 1000000 INFO @ Sun, 21 Jun 2020 19:47:39: 2000000 INFO @ Sun, 21 Jun 2020 19:47:44: 3000000 INFO @ Sun, 21 Jun 2020 19:47:49: 4000000 INFO @ Sun, 21 Jun 2020 19:47:55: 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 19:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.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 19:47:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:00: 6000000 INFO @ Sun, 21 Jun 2020 19:48:03: 1000000 INFO @ Sun, 21 Jun 2020 19:48:06: 7000000 INFO @ Sun, 21 Jun 2020 19:48:10: 2000000 INFO @ Sun, 21 Jun 2020 19:48:11: 8000000 INFO @ Sun, 21 Jun 2020 19:48:16: 3000000 INFO @ Sun, 21 Jun 2020 19:48:17: 9000000 INFO @ Sun, 21 Jun 2020 19:48:22: 4000000 INFO @ Sun, 21 Jun 2020 19:48:22: 10000000 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 19:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.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 19:48:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:28: 11000000 INFO @ Sun, 21 Jun 2020 19:48:29: 5000000 INFO @ Sun, 21 Jun 2020 19:48:33: 1000000 INFO @ Sun, 21 Jun 2020 19:48:33: 12000000 INFO @ Sun, 21 Jun 2020 19:48:35: 6000000 INFO @ Sun, 21 Jun 2020 19:48:39: 2000000 INFO @ Sun, 21 Jun 2020 19:48:39: 13000000 INFO @ Sun, 21 Jun 2020 19:48:41: 7000000 INFO @ Sun, 21 Jun 2020 19:48:45: 3000000 INFO @ Sun, 21 Jun 2020 19:48:45: 14000000 INFO @ Sun, 21 Jun 2020 19:48:47: 8000000 INFO @ Sun, 21 Jun 2020 19:48:50: 4000000 INFO @ Sun, 21 Jun 2020 19:48:51: 15000000 INFO @ Sun, 21 Jun 2020 19:48:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:48:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:48:51: #1 total tags in treatment: 15040992 INFO @ Sun, 21 Jun 2020 19:48:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:51: #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 19:48:52: #1 tags after filtering in treatment: 15040992 INFO @ Sun, 21 Jun 2020 19:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:53: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 19:48:53: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 19:48:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:53: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:48:53: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 21 Jun 2020 19:48:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.05_model.r WARNING @ Sun, 21 Jun 2020 19:48:53: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:48:53: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 21 Jun 2020 19:48:53: #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 19:48:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:54: 9000000 INFO @ Sun, 21 Jun 2020 19:48:56: 5000000 INFO @ Sun, 21 Jun 2020 19:49:00: 10000000 INFO @ Sun, 21 Jun 2020 19:49:02: 6000000 INFO @ Sun, 21 Jun 2020 19:49:06: 11000000 INFO @ Sun, 21 Jun 2020 19:49:08: 7000000 INFO @ Sun, 21 Jun 2020 19:49:12: 12000000 INFO @ Sun, 21 Jun 2020 19:49:13: 8000000 INFO @ Sun, 21 Jun 2020 19:49:19: 13000000 INFO @ Sun, 21 Jun 2020 19:49:19: 9000000 INFO @ Sun, 21 Jun 2020 19:49:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:49:25: 10000000 INFO @ Sun, 21 Jun 2020 19:49:25: 14000000 INFO @ Sun, 21 Jun 2020 19:49:31: 11000000 INFO @ Sun, 21 Jun 2020 19:49:32: 15000000 INFO @ Sun, 21 Jun 2020 19:49:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:49:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:49:32: #1 total tags in treatment: 15040992 INFO @ Sun, 21 Jun 2020 19:49:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:32: #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 19:49:33: #1 tags after filtering in treatment: 15040992 INFO @ Sun, 21 Jun 2020 19:49:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:34: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 19:49:34: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 19:49:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:34: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:49:34: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 21 Jun 2020 19:49:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.10_model.r WARNING @ Sun, 21 Jun 2020 19:49:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:49:34: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 21 Jun 2020 19:49:34: #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 19:49:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:37: 12000000 INFO @ Sun, 21 Jun 2020 19:49:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:49:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:49:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.05_summits.bed INFO @ Sun, 21 Jun 2020 19:49:38: Done! pass1 - making usageList (503 chroms): 1 millis pass2 - checking and writing primary data (2164 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:49:42: 13000000 INFO @ Sun, 21 Jun 2020 19:49:48: 14000000 INFO @ Sun, 21 Jun 2020 19:49:54: 15000000 INFO @ Sun, 21 Jun 2020 19:49:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:49:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:49:54: #1 total tags in treatment: 15040992 INFO @ Sun, 21 Jun 2020 19:49:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:54: #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 19:49:55: #1 tags after filtering in treatment: 15040992 INFO @ Sun, 21 Jun 2020 19:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:56: #2 number of paired peaks: 299 WARNING @ Sun, 21 Jun 2020 19:49:56: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Sun, 21 Jun 2020 19:49:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:56: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:49:56: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 21 Jun 2020 19:49:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.20_model.r WARNING @ Sun, 21 Jun 2020 19:49:56: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:49:56: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 21 Jun 2020 19:49:56: #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 19:49:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.10_summits.bed INFO @ Sun, 21 Jun 2020 19:50:19: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (1306 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:50:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318787/SRX318787.20_summits.bed INFO @ Sun, 21 Jun 2020 19:50:42: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 7 millis CompletedMACS2peakCalling