Job ID = 6459599 SRX = SRX7277040 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:53:07 prefetch.2.10.7: 1) Downloading 'SRR10597305'... 2020-06-21T13:53:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:54:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:54:28 prefetch.2.10.7: 'SRR10597305' is valid 2020-06-21T13:54:28 prefetch.2.10.7: 1) 'SRR10597305' was downloaded successfully 2020-06-21T13:54:28 prefetch.2.10.7: 'SRR10597305' has 0 unresolved dependencies Read 18573065 spots for SRR10597305/SRR10597305.sra Written 18573065 spots for SRR10597305/SRR10597305.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: 00:04:36 18573065 reads; of these: 18573065 (100.00%) were unpaired; of these: 2980860 (16.05%) aligned 0 times 11219982 (60.41%) aligned exactly 1 time 4372223 (23.54%) aligned >1 times 83.95% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 10019135 / 15592205 = 0.6426 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 23:03:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.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 23:03:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:03:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:03:53: 1000000 INFO @ Sun, 21 Jun 2020 23:03:58: 2000000 INFO @ Sun, 21 Jun 2020 23:04:03: 3000000 INFO @ Sun, 21 Jun 2020 23:04:08: 4000000 INFO @ Sun, 21 Jun 2020 23:04:13: 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 23:04:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:04:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:04:17: #1 total tags in treatment: 5573070 INFO @ Sun, 21 Jun 2020 23:04:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:04:17: #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 23:04:17: #1 tags after filtering in treatment: 5573067 INFO @ Sun, 21 Jun 2020 23:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:04:17: #1 finished! INFO @ Sun, 21 Jun 2020 23:04:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:04:18: #2 number of paired peaks: 1617 INFO @ Sun, 21 Jun 2020 23:04:18: start model_add_line... INFO @ Sun, 21 Jun 2020 23:04:18: start X-correlation... INFO @ Sun, 21 Jun 2020 23:04:18: end of X-cor INFO @ Sun, 21 Jun 2020 23:04:18: #2 finished! INFO @ Sun, 21 Jun 2020 23:04:18: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 23:04:18: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 21 Jun 2020 23:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.05_model.r WARNING @ Sun, 21 Jun 2020 23:04:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:04:18: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 21 Jun 2020 23:04:18: #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 23:04:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:04:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.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 23:04:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:04:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:04:23: 1000000 INFO @ Sun, 21 Jun 2020 23:04:28: 2000000 INFO @ Sun, 21 Jun 2020 23:04:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:04:33: 3000000 INFO @ Sun, 21 Jun 2020 23:04:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.05_summits.bed INFO @ Sun, 21 Jun 2020 23:04:35: Done! pass1 - making usageList (727 chroms): 1 millis pass2 - checking and writing primary data (2921 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:04:37: 4000000 INFO @ Sun, 21 Jun 2020 23:04:43: 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 23:04:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:04:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:04:46: #1 total tags in treatment: 5573070 INFO @ Sun, 21 Jun 2020 23:04:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:04:46: #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 23:04:47: #1 tags after filtering in treatment: 5573067 INFO @ Sun, 21 Jun 2020 23:04:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:04:47: #1 finished! INFO @ Sun, 21 Jun 2020 23:04:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:04:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:04:47: #2 number of paired peaks: 1617 INFO @ Sun, 21 Jun 2020 23:04:47: start model_add_line... INFO @ Sun, 21 Jun 2020 23:04:47: start X-correlation... INFO @ Sun, 21 Jun 2020 23:04:47: end of X-cor INFO @ Sun, 21 Jun 2020 23:04:47: #2 finished! INFO @ Sun, 21 Jun 2020 23:04:47: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 23:04:47: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 21 Jun 2020 23:04:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.10_model.r WARNING @ Sun, 21 Jun 2020 23:04:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:04:47: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 21 Jun 2020 23:04:47: #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 23:04:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:04:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:04:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.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 23:04:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:04:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:04:53: 1000000 INFO @ Sun, 21 Jun 2020 23:04:57: 2000000 INFO @ Sun, 21 Jun 2020 23:04:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:05:02: 3000000 INFO @ Sun, 21 Jun 2020 23:05:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:05:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:05:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.10_summits.bed INFO @ Sun, 21 Jun 2020 23:05:04: Done! pass1 - making usageList (580 chroms): 1 millis pass2 - checking and writing primary data (1932 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:05:07: 4000000 INFO @ Sun, 21 Jun 2020 23:05:12: 5000000 INFO @ Sun, 21 Jun 2020 23:05:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:05:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:05:15: #1 total tags in treatment: 5573070 INFO @ Sun, 21 Jun 2020 23:05:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:05:15: #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 23:05:16: #1 tags after filtering in treatment: 5573067 INFO @ Sun, 21 Jun 2020 23:05:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:05:16: #1 finished! INFO @ Sun, 21 Jun 2020 23:05:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:05:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:05:17: #2 number of paired peaks: 1617 INFO @ Sun, 21 Jun 2020 23:05:17: start model_add_line... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:05:17: start X-correlation... INFO @ Sun, 21 Jun 2020 23:05:17: end of X-cor INFO @ Sun, 21 Jun 2020 23:05:17: #2 finished! INFO @ Sun, 21 Jun 2020 23:05:17: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 23:05:17: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 21 Jun 2020 23:05:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.20_model.r WARNING @ Sun, 21 Jun 2020 23:05:17: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:05:17: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 21 Jun 2020 23:05:17: #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 23:05:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:05:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:05:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7277040/SRX7277040.20_summits.bed INFO @ Sun, 21 Jun 2020 23:05:34: Done! BigWig に変換しました。 pass1 - making usageList (292 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 16 millis CompletedMACS2peakCalling