Job ID = 6453369 SRX = SRX1120701 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:19:32 prefetch.2.10.7: 1) Downloading 'SRR2129933'... 2020-06-21T08:19:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:49 prefetch.2.10.7: 1) 'SRR2129933' was downloaded successfully Read 11429559 spots for SRR2129933/SRR2129933.sra Written 11429559 spots for SRR2129933/SRR2129933.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: 00:05:05 11429559 reads; of these: 11429559 (100.00%) were unpaired; of these: 1596186 (13.97%) aligned 0 times 2981181 (26.08%) aligned exactly 1 time 6852192 (59.95%) aligned >1 times 86.03% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 7016151 / 9833373 = 0.7135 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 17:30:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.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 17:30:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:18: 1000000 INFO @ Sun, 21 Jun 2020 17:30:24: 2000000 INFO @ Sun, 21 Jun 2020 17:30:30: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:30:30: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:30:30: #1 total tags in treatment: 2817222 INFO @ Sun, 21 Jun 2020 17:30:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:30: #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 17:30:30: #1 tags after filtering in treatment: 2817107 INFO @ Sun, 21 Jun 2020 17:30:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:30: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:31: #2 number of paired peaks: 9422 INFO @ Sun, 21 Jun 2020 17:30:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:31: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 17:30:31: #2 alternative fragment length(s) may be 4,97 bps INFO @ Sun, 21 Jun 2020 17:30:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.05_model.r WARNING @ Sun, 21 Jun 2020 17:30:31: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:30:31: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Sun, 21 Jun 2020 17:30:31: #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 17:30:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:39: #3 Call peaks for each chromosome... 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 17:30:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.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 17:30:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.05_summits.bed INFO @ Sun, 21 Jun 2020 17:30:43: Done! pass1 - making usageList (1054 chroms): 2 millis pass2 - checking and writing primary data (4825 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:30:48: 1000000 INFO @ Sun, 21 Jun 2020 17:30:55: 2000000 INFO @ Sun, 21 Jun 2020 17:31:00: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:31:00: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:31:00: #1 total tags in treatment: 2817222 INFO @ Sun, 21 Jun 2020 17:31:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:00: #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 17:31:01: #1 tags after filtering in treatment: 2817107 INFO @ Sun, 21 Jun 2020 17:31:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:01: #2 number of paired peaks: 9422 INFO @ Sun, 21 Jun 2020 17:31:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:01: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 17:31:01: #2 alternative fragment length(s) may be 4,97 bps INFO @ Sun, 21 Jun 2020 17:31:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.10_model.r WARNING @ Sun, 21 Jun 2020 17:31:01: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:01: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Sun, 21 Jun 2020 17:31:01: #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 17:31:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:08: #3 Call peaks for each chromosome... 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 17:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.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 17:31:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.10_summits.bed INFO @ Sun, 21 Jun 2020 17:31:11: Done! pass1 - making usageList (815 chroms): 1 millis pass2 - checking and writing primary data (2335 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:31:18: 1000000 INFO @ Sun, 21 Jun 2020 17:31:25: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:31:31: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:31:31: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:31:31: #1 total tags in treatment: 2817222 INFO @ Sun, 21 Jun 2020 17:31:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:31: #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 17:31:31: #1 tags after filtering in treatment: 2817107 INFO @ Sun, 21 Jun 2020 17:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:31: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:31: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:31:32: #2 number of paired peaks: 9422 INFO @ Sun, 21 Jun 2020 17:31:32: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:32: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:32: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:32: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:32: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 17:31:32: #2 alternative fragment length(s) may be 4,97 bps INFO @ Sun, 21 Jun 2020 17:31:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.20_model.r WARNING @ Sun, 21 Jun 2020 17:31:32: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:32: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Sun, 21 Jun 2020 17:31:32: #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 17:31:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120701/SRX1120701.20_summits.bed INFO @ Sun, 21 Jun 2020 17:31:42: Done! pass1 - making usageList (529 chroms): 2 millis pass2 - checking and writing primary data (1136 records, 4 fields): 16 millis CompletedMACS2peakCalling