Job ID = 6455380 SRX = SRX287741 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:10:21 prefetch.2.10.7: 1) Downloading 'SRR869930'... 2020-06-21T10:10:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:14:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:14:25 prefetch.2.10.7: 1) 'SRR869930' was downloaded successfully Read 21266404 spots for SRR869930/SRR869930.sra Written 21266404 spots for SRR869930/SRR869930.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:15 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1611471 (7.58%) aligned 0 times 13447302 (63.23%) aligned exactly 1 time 6207631 (29.19%) aligned >1 times 92.42% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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 12 files... [bam_rmdupse_core] 4582860 / 19654933 = 0.2332 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 19:28:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.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 19:28:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:15: 1000000 INFO @ Sun, 21 Jun 2020 19:28:21: 2000000 INFO @ Sun, 21 Jun 2020 19:28:27: 3000000 INFO @ Sun, 21 Jun 2020 19:28:34: 4000000 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 19:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.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 19:28:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:40: 5000000 INFO @ Sun, 21 Jun 2020 19:28:45: 1000000 INFO @ Sun, 21 Jun 2020 19:28:46: 6000000 INFO @ Sun, 21 Jun 2020 19:28:53: 2000000 INFO @ Sun, 21 Jun 2020 19:28:53: 7000000 INFO @ Sun, 21 Jun 2020 19:28:59: 8000000 INFO @ Sun, 21 Jun 2020 19:29:00: 3000000 INFO @ Sun, 21 Jun 2020 19:29:06: 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 19:29:07: 4000000 INFO @ Sun, 21 Jun 2020 19:29:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.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 19:29:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:12: 10000000 INFO @ Sun, 21 Jun 2020 19:29:15: 5000000 INFO @ Sun, 21 Jun 2020 19:29:17: 1000000 INFO @ Sun, 21 Jun 2020 19:29:20: 11000000 INFO @ Sun, 21 Jun 2020 19:29:24: 6000000 INFO @ Sun, 21 Jun 2020 19:29:26: 2000000 INFO @ Sun, 21 Jun 2020 19:29:28: 12000000 INFO @ Sun, 21 Jun 2020 19:29:32: 7000000 INFO @ Sun, 21 Jun 2020 19:29:34: 3000000 INFO @ Sun, 21 Jun 2020 19:29:36: 13000000 INFO @ Sun, 21 Jun 2020 19:29:40: 8000000 INFO @ Sun, 21 Jun 2020 19:29:42: 4000000 INFO @ Sun, 21 Jun 2020 19:29:44: 14000000 INFO @ Sun, 21 Jun 2020 19:29:48: 9000000 INFO @ Sun, 21 Jun 2020 19:29:51: 5000000 INFO @ Sun, 21 Jun 2020 19:29:53: 15000000 INFO @ Sun, 21 Jun 2020 19:29:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:54: #1 total tags in treatment: 15072073 INFO @ Sun, 21 Jun 2020 19:29:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:54: #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 19:29:54: #1 tags after filtering in treatment: 15072073 INFO @ Sun, 21 Jun 2020 19:29:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:55: #2 number of paired peaks: 725 WARNING @ Sun, 21 Jun 2020 19:29:55: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Sun, 21 Jun 2020 19:29:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:56: #2 predicted fragment length is 33 bps INFO @ Sun, 21 Jun 2020 19:29:56: #2 alternative fragment length(s) may be 3,33 bps INFO @ Sun, 21 Jun 2020 19:29:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.05_model.r WARNING @ Sun, 21 Jun 2020 19:29:56: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:29:56: #2 You may need to consider one of the other alternative d(s): 3,33 WARNING @ Sun, 21 Jun 2020 19:29:56: #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 19:29:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:56: 10000000 INFO @ Sun, 21 Jun 2020 19:29:59: 6000000 INFO @ Sun, 21 Jun 2020 19:30:04: 11000000 INFO @ Sun, 21 Jun 2020 19:30:07: 7000000 INFO @ Sun, 21 Jun 2020 19:30:12: 12000000 INFO @ Sun, 21 Jun 2020 19:30:15: 8000000 INFO @ Sun, 21 Jun 2020 19:30:20: 13000000 INFO @ Sun, 21 Jun 2020 19:30:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:23: 9000000 INFO @ Sun, 21 Jun 2020 19:30:28: 14000000 INFO @ Sun, 21 Jun 2020 19:30:31: 10000000 INFO @ Sun, 21 Jun 2020 19:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.05_summits.bed INFO @ Sun, 21 Jun 2020 19:30:35: Done! pass1 - making usageList (641 chroms): 2 millis pass2 - checking and writing primary data (2441 records, 4 fields): 39 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:30:36: 15000000 INFO @ Sun, 21 Jun 2020 19:30:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:37: #1 total tags in treatment: 15072073 INFO @ Sun, 21 Jun 2020 19:30:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:37: #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 19:30:37: #1 tags after filtering in treatment: 15072073 INFO @ Sun, 21 Jun 2020 19:30:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:39: #2 number of paired peaks: 725 WARNING @ Sun, 21 Jun 2020 19:30:39: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:39: #2 predicted fragment length is 33 bps INFO @ Sun, 21 Jun 2020 19:30:39: #2 alternative fragment length(s) may be 3,33 bps INFO @ Sun, 21 Jun 2020 19:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.10_model.r WARNING @ Sun, 21 Jun 2020 19:30:39: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:30:39: #2 You may need to consider one of the other alternative d(s): 3,33 WARNING @ Sun, 21 Jun 2020 19:30:39: #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 19:30:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:39: 11000000 INFO @ Sun, 21 Jun 2020 19:30:47: 12000000 INFO @ Sun, 21 Jun 2020 19:30:53: 13000000 INFO @ Sun, 21 Jun 2020 19:31:01: 14000000 INFO @ Sun, 21 Jun 2020 19:31:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:10: 15000000 INFO @ Sun, 21 Jun 2020 19:31:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:10: #1 total tags in treatment: 15072073 INFO @ Sun, 21 Jun 2020 19:31:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:10: #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 19:31:11: #1 tags after filtering in treatment: 15072073 INFO @ Sun, 21 Jun 2020 19:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:12: #2 number of paired peaks: 725 WARNING @ Sun, 21 Jun 2020 19:31:12: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:12: #2 predicted fragment length is 33 bps INFO @ Sun, 21 Jun 2020 19:31:12: #2 alternative fragment length(s) may be 3,33 bps INFO @ Sun, 21 Jun 2020 19:31:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.20_model.r WARNING @ Sun, 21 Jun 2020 19:31:12: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:31:12: #2 You may need to consider one of the other alternative d(s): 3,33 WARNING @ Sun, 21 Jun 2020 19:31:12: #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 19:31:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:31:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.10_summits.bed INFO @ Sun, 21 Jun 2020 19:31:19: Done! pass1 - making usageList (507 chroms): 1 millis pass2 - checking and writing primary data (1975 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287741/SRX287741.20_summits.bed INFO @ Sun, 21 Jun 2020 19:31:53: Done! pass1 - making usageList (326 chroms): 1 millis pass2 - checking and writing primary data (709 records, 4 fields): 19 millis CompletedMACS2peakCalling