Job ID = 6455487 SRX = SRX287826 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:01:41 prefetch.2.10.7: 1) Downloading 'SRR870015'... 2020-06-21T10:01:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:03:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:03:50 prefetch.2.10.7: 1) 'SRR870015' was downloaded successfully Read 17133552 spots for SRR870015/SRR870015.sra Written 17133552 spots for SRR870015/SRR870015.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: 00:05:18 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 963641 (5.62%) aligned 0 times 11195554 (65.34%) aligned exactly 1 time 4974357 (29.03%) aligned >1 times 94.38% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 2734999 / 16169911 = 0.1691 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 19:14:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.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 19:14:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:21: 1000000 INFO @ Sun, 21 Jun 2020 19:14:28: 2000000 INFO @ Sun, 21 Jun 2020 19:14:35: 3000000 INFO @ Sun, 21 Jun 2020 19:14:42: 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 19:14:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.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 19:14:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:50: 5000000 INFO @ Sun, 21 Jun 2020 19:14:51: 1000000 INFO @ Sun, 21 Jun 2020 19:14:57: 6000000 INFO @ Sun, 21 Jun 2020 19:14:58: 2000000 INFO @ Sun, 21 Jun 2020 19:15:05: 7000000 INFO @ Sun, 21 Jun 2020 19:15:05: 3000000 INFO @ Sun, 21 Jun 2020 19:15:12: 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 19:15:13: 8000000 INFO @ Sun, 21 Jun 2020 19:15:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.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 19:15:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:19: 5000000 INFO @ Sun, 21 Jun 2020 19:15:21: 9000000 INFO @ Sun, 21 Jun 2020 19:15:22: 1000000 INFO @ Sun, 21 Jun 2020 19:15:26: 6000000 INFO @ Sun, 21 Jun 2020 19:15:29: 2000000 INFO @ Sun, 21 Jun 2020 19:15:29: 10000000 INFO @ Sun, 21 Jun 2020 19:15:33: 7000000 INFO @ Sun, 21 Jun 2020 19:15:36: 3000000 INFO @ Sun, 21 Jun 2020 19:15:37: 11000000 INFO @ Sun, 21 Jun 2020 19:15:40: 8000000 INFO @ Sun, 21 Jun 2020 19:15:43: 4000000 INFO @ Sun, 21 Jun 2020 19:15:46: 12000000 INFO @ Sun, 21 Jun 2020 19:15:48: 9000000 INFO @ Sun, 21 Jun 2020 19:15:51: 5000000 INFO @ Sun, 21 Jun 2020 19:15:54: 13000000 INFO @ Sun, 21 Jun 2020 19:15:55: 10000000 INFO @ Sun, 21 Jun 2020 19:15:58: 6000000 INFO @ Sun, 21 Jun 2020 19:15:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:58: #1 total tags in treatment: 13434912 INFO @ Sun, 21 Jun 2020 19:15:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:58: #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 19:15:59: #1 tags after filtering in treatment: 13434912 INFO @ Sun, 21 Jun 2020 19:15:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:00: #2 number of paired peaks: 444 WARNING @ Sun, 21 Jun 2020 19:16:00: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:00: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:16:00: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 21 Jun 2020 19:16:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.05_model.r WARNING @ Sun, 21 Jun 2020 19:16:00: #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 19:16:00: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 21 Jun 2020 19:16:00: #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 19:16:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:02: 11000000 INFO @ Sun, 21 Jun 2020 19:16:05: 7000000 INFO @ Sun, 21 Jun 2020 19:16:10: 12000000 INFO @ Sun, 21 Jun 2020 19:16:12: 8000000 INFO @ Sun, 21 Jun 2020 19:16:17: 13000000 INFO @ Sun, 21 Jun 2020 19:16:19: 9000000 INFO @ Sun, 21 Jun 2020 19:16:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:20: #1 total tags in treatment: 13434912 INFO @ Sun, 21 Jun 2020 19:16:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:20: #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 19:16:21: #1 tags after filtering in treatment: 13434912 INFO @ Sun, 21 Jun 2020 19:16:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:22: #2 number of paired peaks: 444 WARNING @ Sun, 21 Jun 2020 19:16:22: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:22: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:16:22: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 21 Jun 2020 19:16:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.10_model.r WARNING @ Sun, 21 Jun 2020 19:16:22: #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 19:16:22: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 21 Jun 2020 19:16:22: #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 19:16:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:22: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:16:26: 10000000 INFO @ Sun, 21 Jun 2020 19:16:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:32: 11000000 INFO @ Sun, 21 Jun 2020 19:16:39: 12000000 INFO @ Sun, 21 Jun 2020 19:16:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.05_summits.bed INFO @ Sun, 21 Jun 2020 19:16:43: Done! pass1 - making usageList (615 chroms): 2 millis pass2 - checking and writing primary data (2507 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:45: 13000000 INFO @ Sun, 21 Jun 2020 19:16:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:48: #1 total tags in treatment: 13434912 INFO @ Sun, 21 Jun 2020 19:16:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:48: #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 19:16:49: #1 tags after filtering in treatment: 13434912 INFO @ Sun, 21 Jun 2020 19:16:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:50: #2 number of paired peaks: 444 WARNING @ Sun, 21 Jun 2020 19:16:50: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:50: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:16:50: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 21 Jun 2020 19:16:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.20_model.r WARNING @ Sun, 21 Jun 2020 19:16:50: #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 19:16:50: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 21 Jun 2020 19:16:50: #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 19:16:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:17:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.10_summits.bed INFO @ Sun, 21 Jun 2020 19:17:05: Done! pass1 - making usageList (501 chroms): 1 millis pass2 - checking and writing primary data (1693 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:17:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287826/SRX287826.20_summits.bed INFO @ Sun, 21 Jun 2020 19:17:34: Done! pass1 - making usageList (253 chroms): 1 millis pass2 - checking and writing primary data (517 records, 4 fields): 9 millis CompletedMACS2peakCalling