Job ID = 6458451 SRX = SRX5227005 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:52 prefetch.2.10.7: 1) Downloading 'SRR8417920'... 2020-06-21T12:30:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:33:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:33:43 prefetch.2.10.7: 'SRR8417920' is valid 2020-06-21T12:33:43 prefetch.2.10.7: 1) 'SRR8417920' was downloaded successfully 2020-06-21T12:33:43 prefetch.2.10.7: 'SRR8417920' has 0 unresolved dependencies Read 11457696 spots for SRR8417920/SRR8417920.sra Written 11457696 spots for SRR8417920/SRR8417920.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: 00:04:00 11457696 reads; of these: 11457696 (100.00%) were unpaired; of these: 827692 (7.22%) aligned 0 times 8228170 (71.81%) aligned exactly 1 time 2401834 (20.96%) aligned >1 times 92.78% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 703804 / 10630004 = 0.0662 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 21:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.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 21:42:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:30: 1000000 INFO @ Sun, 21 Jun 2020 21:42:36: 2000000 INFO @ Sun, 21 Jun 2020 21:42:41: 3000000 INFO @ Sun, 21 Jun 2020 21:42:46: 4000000 INFO @ Sun, 21 Jun 2020 21:42:51: 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 21:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.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 21:42:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:56: 6000000 INFO @ Sun, 21 Jun 2020 21:43:00: 1000000 INFO @ Sun, 21 Jun 2020 21:43:01: 7000000 INFO @ Sun, 21 Jun 2020 21:43:06: 2000000 INFO @ Sun, 21 Jun 2020 21:43:07: 8000000 INFO @ Sun, 21 Jun 2020 21:43:11: 3000000 INFO @ Sun, 21 Jun 2020 21:43:12: 9000000 INFO @ Sun, 21 Jun 2020 21:43:16: 4000000 INFO @ Sun, 21 Jun 2020 21:43:17: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:43:17: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:43:17: #1 total tags in treatment: 9926200 INFO @ Sun, 21 Jun 2020 21:43:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:17: #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 21:43:18: #1 tags after filtering in treatment: 9926125 INFO @ Sun, 21 Jun 2020 21:43:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:19: #2 number of paired peaks: 536 WARNING @ Sun, 21 Jun 2020 21:43:19: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sun, 21 Jun 2020 21:43:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:19: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 21:43:19: #2 alternative fragment length(s) may be 4,82,576 bps INFO @ Sun, 21 Jun 2020 21:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.05_model.r WARNING @ Sun, 21 Jun 2020 21:43:19: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:19: #2 You may need to consider one of the other alternative d(s): 4,82,576 WARNING @ Sun, 21 Jun 2020 21:43:19: #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 21:43:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:43:21: 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 21:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.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 21:43:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:43:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:43:27: 6000000 INFO @ Sun, 21 Jun 2020 21:43:30: 1000000 INFO @ Sun, 21 Jun 2020 21:43:32: 7000000 INFO @ Sun, 21 Jun 2020 21:43:36: 2000000 INFO @ Sun, 21 Jun 2020 21:43:37: 8000000 INFO @ Sun, 21 Jun 2020 21:43:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:41: 3000000 INFO @ Sun, 21 Jun 2020 21:43:43: 9000000 INFO @ Sun, 21 Jun 2020 21:43:47: 4000000 INFO @ Sun, 21 Jun 2020 21:43:48: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:43:48: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:43:48: #1 total tags in treatment: 9926200 INFO @ Sun, 21 Jun 2020 21:43:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:48: #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 21:43:49: #1 tags after filtering in treatment: 9926125 INFO @ Sun, 21 Jun 2020 21:43:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:49: #2 number of paired peaks: 536 WARNING @ Sun, 21 Jun 2020 21:43:49: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sun, 21 Jun 2020 21:43:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:49: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 21:43:49: #2 alternative fragment length(s) may be 4,82,576 bps INFO @ Sun, 21 Jun 2020 21:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.10_model.r WARNING @ Sun, 21 Jun 2020 21:43:49: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:49: #2 You may need to consider one of the other alternative d(s): 4,82,576 WARNING @ Sun, 21 Jun 2020 21:43:49: #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 21:43:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:43:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.05_summits.bed INFO @ Sun, 21 Jun 2020 21:43:50: Done! pass1 - making usageList (574 chroms): 1 millis pass2 - checking and writing primary data (2070 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:43:52: 5000000 INFO @ Sun, 21 Jun 2020 21:43:57: 6000000 INFO @ Sun, 21 Jun 2020 21:44:02: 7000000 INFO @ Sun, 21 Jun 2020 21:44:08: 8000000 INFO @ Sun, 21 Jun 2020 21:44:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:44:13: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:44:18: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:44:18: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:44:18: #1 total tags in treatment: 9926200 INFO @ Sun, 21 Jun 2020 21:44:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:44:18: #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 21:44:19: #1 tags after filtering in treatment: 9926125 INFO @ Sun, 21 Jun 2020 21:44:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:44:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:44:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:44:19: #2 number of paired peaks: 536 WARNING @ Sun, 21 Jun 2020 21:44:19: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sun, 21 Jun 2020 21:44:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:44:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:44:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:44:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:44:19: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 21:44:19: #2 alternative fragment length(s) may be 4,82,576 bps INFO @ Sun, 21 Jun 2020 21:44:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.20_model.r WARNING @ Sun, 21 Jun 2020 21:44:19: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:44:19: #2 You may need to consider one of the other alternative d(s): 4,82,576 WARNING @ Sun, 21 Jun 2020 21:44:19: #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 21:44:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.10_summits.bed INFO @ Sun, 21 Jun 2020 21:44:20: Done! pass1 - making usageList (395 chroms): 1 millis pass2 - checking and writing primary data (978 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:44:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227005/SRX5227005.20_summits.bed INFO @ Sun, 21 Jun 2020 21:44:50: Done! pass1 - making usageList (202 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 7 millis CompletedMACS2peakCalling