Job ID = 6454695 SRX = SRX2520644 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:27:14 prefetch.2.10.7: 1) Downloading 'SRR5206763'... 2020-06-21T09:27:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:29:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:29:12 prefetch.2.10.7: 'SRR5206763' is valid 2020-06-21T09:29:12 prefetch.2.10.7: 1) 'SRR5206763' was downloaded successfully Read 15204899 spots for SRR5206763/SRR5206763.sra Written 15204899 spots for SRR5206763/SRR5206763.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: 00:00:01 Multiseed full-index search: 00:04:04 15204899 reads; of these: 15204899 (100.00%) were unpaired; of these: 353263 (2.32%) aligned 0 times 10373137 (68.22%) aligned exactly 1 time 4478499 (29.45%) aligned >1 times 97.68% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 3596997 / 14851636 = 0.2422 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 18:37:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.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 18:37:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:33: 1000000 INFO @ Sun, 21 Jun 2020 18:37:38: 2000000 INFO @ Sun, 21 Jun 2020 18:37:44: 3000000 INFO @ Sun, 21 Jun 2020 18:37:49: 4000000 INFO @ Sun, 21 Jun 2020 18:37:54: 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 18:37:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.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 18:37:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:58: 6000000 INFO @ Sun, 21 Jun 2020 18:38:03: 1000000 INFO @ Sun, 21 Jun 2020 18:38:03: 7000000 INFO @ Sun, 21 Jun 2020 18:38:08: 2000000 INFO @ Sun, 21 Jun 2020 18:38:08: 8000000 INFO @ Sun, 21 Jun 2020 18:38:13: 3000000 INFO @ Sun, 21 Jun 2020 18:38:13: 9000000 INFO @ Sun, 21 Jun 2020 18:38:18: 4000000 INFO @ Sun, 21 Jun 2020 18:38:19: 10000000 INFO @ Sun, 21 Jun 2020 18:38:23: 5000000 INFO @ Sun, 21 Jun 2020 18:38:24: 11000000 INFO @ Sun, 21 Jun 2020 18:38:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:38:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:38:25: #1 total tags in treatment: 11254639 INFO @ Sun, 21 Jun 2020 18:38:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:25: #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 18:38:26: #1 tags after filtering in treatment: 11254548 INFO @ Sun, 21 Jun 2020 18:38:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:26: #2 looking for paired plus/minus strand peaks... 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 18:38:26: #2 number of paired peaks: 425 WARNING @ Sun, 21 Jun 2020 18:38:26: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 21 Jun 2020 18:38:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:26: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 18:38:26: #2 alternative fragment length(s) may be 3,54,79,97,507,556,571 bps INFO @ Sun, 21 Jun 2020 18:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.05_model.r WARNING @ Sun, 21 Jun 2020 18:38:26: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:38:26: #2 You may need to consider one of the other alternative d(s): 3,54,79,97,507,556,571 WARNING @ Sun, 21 Jun 2020 18:38:26: #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 18:38:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:27: 6000000 INFO @ Sun, 21 Jun 2020 18:38:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.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 18:38:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:32: 7000000 INFO @ Sun, 21 Jun 2020 18:38:33: 1000000 INFO @ Sun, 21 Jun 2020 18:38:37: 8000000 INFO @ Sun, 21 Jun 2020 18:38:38: 2000000 INFO @ Sun, 21 Jun 2020 18:38:42: 9000000 INFO @ Sun, 21 Jun 2020 18:38:43: 3000000 INFO @ Sun, 21 Jun 2020 18:38:47: 10000000 INFO @ Sun, 21 Jun 2020 18:38:48: 4000000 INFO @ Sun, 21 Jun 2020 18:38:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:38:52: 11000000 INFO @ Sun, 21 Jun 2020 18:38:52: 5000000 INFO @ Sun, 21 Jun 2020 18:38:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:38:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:38:53: #1 total tags in treatment: 11254639 INFO @ Sun, 21 Jun 2020 18:38:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:53: #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 18:38:54: #1 tags after filtering in treatment: 11254548 INFO @ Sun, 21 Jun 2020 18:38:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:55: #2 number of paired peaks: 425 WARNING @ Sun, 21 Jun 2020 18:38:55: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 21 Jun 2020 18:38:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:55: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 18:38:55: #2 alternative fragment length(s) may be 3,54,79,97,507,556,571 bps INFO @ Sun, 21 Jun 2020 18:38:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.10_model.r WARNING @ Sun, 21 Jun 2020 18:38:55: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:38:55: #2 You may need to consider one of the other alternative d(s): 3,54,79,97,507,556,571 WARNING @ Sun, 21 Jun 2020 18:38:55: #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 18:38:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:57: 6000000 INFO @ Sun, 21 Jun 2020 18:38:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.05_summits.bed INFO @ Sun, 21 Jun 2020 18:38:59: Done! pass1 - making usageList (328 chroms): 1 millis pass2 - checking and writing primary data (1236 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:02: 7000000 INFO @ Sun, 21 Jun 2020 18:39:07: 8000000 INFO @ Sun, 21 Jun 2020 18:39:11: 9000000 INFO @ Sun, 21 Jun 2020 18:39:17: 10000000 INFO @ Sun, 21 Jun 2020 18:39:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:21: 11000000 INFO @ Sun, 21 Jun 2020 18:39:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:39:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:39:23: #1 total tags in treatment: 11254639 INFO @ Sun, 21 Jun 2020 18:39:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:23: #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 18:39:23: #1 tags after filtering in treatment: 11254548 INFO @ Sun, 21 Jun 2020 18:39:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:24: #2 number of paired peaks: 425 WARNING @ Sun, 21 Jun 2020 18:39:24: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 21 Jun 2020 18:39:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:24: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 18:39:24: #2 alternative fragment length(s) may be 3,54,79,97,507,556,571 bps INFO @ Sun, 21 Jun 2020 18:39:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.20_model.r WARNING @ Sun, 21 Jun 2020 18:39:24: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:24: #2 You may need to consider one of the other alternative d(s): 3,54,79,97,507,556,571 WARNING @ Sun, 21 Jun 2020 18:39:24: #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 18:39:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:39:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.10_summits.bed INFO @ Sun, 21 Jun 2020 18:39:29: Done! pass1 - making usageList (150 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:39:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520644/SRX2520644.20_summits.bed INFO @ Sun, 21 Jun 2020 18:39:57: Done! pass1 - making usageList (77 chroms): 0 millis pass2 - checking and writing primary data (137 records, 4 fields): 4 millis CompletedMACS2peakCalling