Job ID = 6455695 SRX = SRX287996 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:15:21 prefetch.2.10.7: 1) Downloading 'SRR870185'... 2020-06-21T10:15:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:58 prefetch.2.10.7: 1) 'SRR870185' was downloaded successfully Read 18953572 spots for SRR870185/SRR870185.sra Written 18953572 spots for SRR870185/SRR870185.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: 00:06:34 18953572 reads; of these: 18953572 (100.00%) were unpaired; of these: 1311870 (6.92%) aligned 0 times 11692932 (61.69%) aligned exactly 1 time 5948770 (31.39%) aligned >1 times 93.08% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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] 3506802 / 17641702 = 0.1988 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 19:33:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.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 19:33:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:27: 1000000 INFO @ Sun, 21 Jun 2020 19:33:34: 2000000 INFO @ Sun, 21 Jun 2020 19:33:41: 3000000 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 19:33:48: 4000000 INFO @ Sun, 21 Jun 2020 19:33:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.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 19:33:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:55: 5000000 INFO @ Sun, 21 Jun 2020 19:33:56: 1000000 INFO @ Sun, 21 Jun 2020 19:34:01: 2000000 INFO @ Sun, 21 Jun 2020 19:34:02: 6000000 INFO @ Sun, 21 Jun 2020 19:34:07: 3000000 INFO @ Sun, 21 Jun 2020 19:34:09: 7000000 INFO @ Sun, 21 Jun 2020 19:34:12: 4000000 INFO @ Sun, 21 Jun 2020 19:34:16: 8000000 INFO @ Sun, 21 Jun 2020 19:34:18: 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 19:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.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 19:34:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:22: 9000000 INFO @ Sun, 21 Jun 2020 19:34:23: 6000000 INFO @ Sun, 21 Jun 2020 19:34:28: 1000000 INFO @ Sun, 21 Jun 2020 19:34:29: 10000000 INFO @ Sun, 21 Jun 2020 19:34:29: 7000000 INFO @ Sun, 21 Jun 2020 19:34:34: 2000000 INFO @ Sun, 21 Jun 2020 19:34:35: 8000000 INFO @ Sun, 21 Jun 2020 19:34:36: 11000000 INFO @ Sun, 21 Jun 2020 19:34:39: 3000000 INFO @ Sun, 21 Jun 2020 19:34:41: 9000000 INFO @ Sun, 21 Jun 2020 19:34:43: 12000000 INFO @ Sun, 21 Jun 2020 19:34:45: 4000000 INFO @ Sun, 21 Jun 2020 19:34:47: 10000000 INFO @ Sun, 21 Jun 2020 19:34:49: 13000000 INFO @ Sun, 21 Jun 2020 19:34:51: 5000000 INFO @ Sun, 21 Jun 2020 19:34:53: 11000000 INFO @ Sun, 21 Jun 2020 19:34:55: 14000000 INFO @ Sun, 21 Jun 2020 19:34:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:56: #1 total tags in treatment: 14134900 INFO @ Sun, 21 Jun 2020 19:34:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:56: #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 19:34:57: #1 tags after filtering in treatment: 14134900 INFO @ Sun, 21 Jun 2020 19:34:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:57: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:57: 6000000 INFO @ Sun, 21 Jun 2020 19:34:58: #2 number of paired peaks: 698 WARNING @ Sun, 21 Jun 2020 19:34:58: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:58: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:58: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:58: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 19:34:58: #2 alternative fragment length(s) may be 3,37,552,572 bps INFO @ Sun, 21 Jun 2020 19:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.05_model.r WARNING @ Sun, 21 Jun 2020 19:34:58: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:58: #2 You may need to consider one of the other alternative d(s): 3,37,552,572 WARNING @ Sun, 21 Jun 2020 19:34:58: #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 19:34:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:00: 12000000 INFO @ Sun, 21 Jun 2020 19:35:03: 7000000 INFO @ Sun, 21 Jun 2020 19:35:06: 13000000 INFO @ Sun, 21 Jun 2020 19:35:09: 8000000 INFO @ Sun, 21 Jun 2020 19:35:12: 14000000 INFO @ Sun, 21 Jun 2020 19:35:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:13: #1 total tags in treatment: 14134900 INFO @ Sun, 21 Jun 2020 19:35:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:13: #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 19:35:14: #1 tags after filtering in treatment: 14134900 INFO @ Sun, 21 Jun 2020 19:35:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:15: 9000000 INFO @ Sun, 21 Jun 2020 19:35:15: #2 number of paired peaks: 698 WARNING @ Sun, 21 Jun 2020 19:35:15: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:15: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 19:35:15: #2 alternative fragment length(s) may be 3,37,552,572 bps INFO @ Sun, 21 Jun 2020 19:35:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.10_model.r WARNING @ Sun, 21 Jun 2020 19:35:15: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:15: #2 You may need to consider one of the other alternative d(s): 3,37,552,572 WARNING @ Sun, 21 Jun 2020 19:35:15: #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 19:35:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:20: 10000000 INFO @ Sun, 21 Jun 2020 19:35:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:25: 11000000 INFO @ Sun, 21 Jun 2020 19:35:32: 12000000 INFO @ Sun, 21 Jun 2020 19:35:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.05_summits.bed INFO @ Sun, 21 Jun 2020 19:35:36: Done! pass1 - making usageList (613 chroms): 1 millis pass2 - checking and writing primary data (2419 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:37: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:35:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:42: 14000000 INFO @ Sun, 21 Jun 2020 19:35:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:43: #1 total tags in treatment: 14134900 INFO @ Sun, 21 Jun 2020 19:35:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:43: #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 19:35:44: #1 tags after filtering in treatment: 14134900 INFO @ Sun, 21 Jun 2020 19:35:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:45: #2 number of paired peaks: 698 WARNING @ Sun, 21 Jun 2020 19:35:45: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:45: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 19:35:45: #2 alternative fragment length(s) may be 3,37,552,572 bps INFO @ Sun, 21 Jun 2020 19:35:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.20_model.r WARNING @ Sun, 21 Jun 2020 19:35:45: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:45: #2 You may need to consider one of the other alternative d(s): 3,37,552,572 WARNING @ Sun, 21 Jun 2020 19:35:45: #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 19:35:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.10_summits.bed INFO @ Sun, 21 Jun 2020 19:35:54: Done! pass1 - making usageList (512 chroms): 1 millis pass2 - checking and writing primary data (1983 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287996/SRX287996.20_summits.bed INFO @ Sun, 21 Jun 2020 19:36:23: Done! pass1 - making usageList (344 chroms): 2 millis pass2 - checking and writing primary data (785 records, 4 fields): 20 millis CompletedMACS2peakCalling