Job ID = 6455708 SRX = SRX288008 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:13:21 prefetch.2.10.7: 1) Downloading 'SRR870197'... 2020-06-21T10:13:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:18:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:18:16 prefetch.2.10.7: 1) 'SRR870197' was downloaded successfully Read 18953572 spots for SRR870197/SRR870197.sra Written 18953572 spots for SRR870197/SRR870197.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: 00:05:58 18953572 reads; of these: 18953572 (100.00%) were unpaired; of these: 1311783 (6.92%) aligned 0 times 11692990 (61.69%) aligned exactly 1 time 5948799 (31.39%) aligned >1 times 93.08% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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] 3505948 / 17641789 = 0.1987 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 19:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.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 19:29:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:52: 1000000 INFO @ Sun, 21 Jun 2020 19:29:58: 2000000 INFO @ Sun, 21 Jun 2020 19:30:03: 3000000 INFO @ Sun, 21 Jun 2020 19:30:08: 4000000 INFO @ Sun, 21 Jun 2020 19:30:14: 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 19:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.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 19:30:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:19: 6000000 INFO @ Sun, 21 Jun 2020 19:30:22: 1000000 INFO @ Sun, 21 Jun 2020 19:30:25: 7000000 INFO @ Sun, 21 Jun 2020 19:30:28: 2000000 INFO @ Sun, 21 Jun 2020 19:30:30: 8000000 INFO @ Sun, 21 Jun 2020 19:30:33: 3000000 INFO @ Sun, 21 Jun 2020 19:30:36: 9000000 INFO @ Sun, 21 Jun 2020 19:30:38: 4000000 INFO @ Sun, 21 Jun 2020 19:30:42: 10000000 INFO @ Sun, 21 Jun 2020 19:30:44: 5000000 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 19:30:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.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 19:30:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:48: 11000000 INFO @ Sun, 21 Jun 2020 19:30:49: 6000000 INFO @ Sun, 21 Jun 2020 19:30:51: 1000000 INFO @ Sun, 21 Jun 2020 19:30:54: 12000000 INFO @ Sun, 21 Jun 2020 19:30:55: 7000000 INFO @ Sun, 21 Jun 2020 19:30:56: 2000000 INFO @ Sun, 21 Jun 2020 19:30:59: 13000000 INFO @ Sun, 21 Jun 2020 19:31:00: 8000000 INFO @ Sun, 21 Jun 2020 19:31:01: 3000000 INFO @ Sun, 21 Jun 2020 19:31:05: 14000000 INFO @ Sun, 21 Jun 2020 19:31:06: 4000000 INFO @ Sun, 21 Jun 2020 19:31:06: 9000000 INFO @ Sun, 21 Jun 2020 19:31:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:06: #1 total tags in treatment: 14135841 INFO @ Sun, 21 Jun 2020 19:31:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:06: #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 19:31:07: #1 tags after filtering in treatment: 14135841 INFO @ Sun, 21 Jun 2020 19:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:08: #2 number of paired peaks: 680 WARNING @ Sun, 21 Jun 2020 19:31:08: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:08: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:31:08: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:31:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.05_model.r WARNING @ Sun, 21 Jun 2020 19:31:08: #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 19:31:08: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:31:08: #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 19:31:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:10: 5000000 INFO @ Sun, 21 Jun 2020 19:31:11: 10000000 INFO @ Sun, 21 Jun 2020 19:31:15: 6000000 INFO @ Sun, 21 Jun 2020 19:31:17: 11000000 INFO @ Sun, 21 Jun 2020 19:31:20: 7000000 INFO @ Sun, 21 Jun 2020 19:31:23: 12000000 INFO @ Sun, 21 Jun 2020 19:31:25: 8000000 INFO @ Sun, 21 Jun 2020 19:31:29: 13000000 INFO @ Sun, 21 Jun 2020 19:31:29: 9000000 INFO @ Sun, 21 Jun 2020 19:31:34: 14000000 INFO @ Sun, 21 Jun 2020 19:31:34: 10000000 INFO @ Sun, 21 Jun 2020 19:31:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:35: #1 total tags in treatment: 14135841 INFO @ Sun, 21 Jun 2020 19:31:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:35: #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 19:31:36: #1 tags after filtering in treatment: 14135841 INFO @ Sun, 21 Jun 2020 19:31:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:37: #2 number of paired peaks: 680 WARNING @ Sun, 21 Jun 2020 19:31:37: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:37: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:31:37: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.10_model.r WARNING @ Sun, 21 Jun 2020 19:31:37: #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 19:31:37: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:31:37: #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 19:31:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:39: 11000000 INFO @ Sun, 21 Jun 2020 19:31:45: 12000000 INFO @ Sun, 21 Jun 2020 19:31:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.05_summits.bed INFO @ Sun, 21 Jun 2020 19:31:48: Done! pass1 - making usageList (637 chroms): 2 millis pass2 - checking and writing primary data (2408 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:49: 13000000 INFO @ Sun, 21 Jun 2020 19:31:54: 14000000 INFO @ Sun, 21 Jun 2020 19:31:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:55: #1 total tags in treatment: 14135841 INFO @ Sun, 21 Jun 2020 19:31:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:55: #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 19:31:56: #1 tags after filtering in treatment: 14135841 INFO @ Sun, 21 Jun 2020 19:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:57: #2 number of paired peaks: 680 WARNING @ Sun, 21 Jun 2020 19:31:57: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:57: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 19:31:57: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sun, 21 Jun 2020 19:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.20_model.r WARNING @ Sun, 21 Jun 2020 19:31:57: #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 19:31:57: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sun, 21 Jun 2020 19:31:57: #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 19:31:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:32:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.10_summits.bed INFO @ Sun, 21 Jun 2020 19:32:20: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (1973 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:32:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX288008/SRX288008.20_summits.bed INFO @ Sun, 21 Jun 2020 19:32:37: Done! pass1 - making usageList (354 chroms): 1 millis pass2 - checking and writing primary data (817 records, 4 fields): 11 millis CompletedMACS2peakCalling