Job ID = 6456193 SRX = SRX3293410 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:53 prefetch.2.10.7: 1) Downloading 'SRR6183237'... 2020-06-21T10:30:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:49:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:49:49 prefetch.2.10.7: 1) 'SRR6183237' was downloaded successfully 2020-06-21T10:49:49 prefetch.2.10.7: 'SRR6183237' has 0 unresolved dependencies Read 25001054 spots for SRR6183237/SRR6183237.sra Written 25001054 spots for SRR6183237/SRR6183237.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: 00:59:22 25001054 reads; of these: 25001054 (100.00%) were unpaired; of these: 18991353 (75.96%) aligned 0 times 1508056 (6.03%) aligned exactly 1 time 4501645 (18.01%) aligned >1 times 24.04% overall alignment rate Time searching: 00:59:22 Overall time: 00:59:22 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] 4484643 / 6009701 = 0.7462 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 20:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.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 20:56:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:56:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:56:32: 1000000 INFO @ Sun, 21 Jun 2020 20:56:39: #1 tag size is determined as 250 bps INFO @ Sun, 21 Jun 2020 20:56:39: #1 tag size = 250 INFO @ Sun, 21 Jun 2020 20:56:39: #1 total tags in treatment: 1525058 INFO @ Sun, 21 Jun 2020 20:56:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:56:39: #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 20:56:39: #1 tags after filtering in treatment: 1524795 INFO @ Sun, 21 Jun 2020 20:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:56:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:56:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:56:39: #2 number of paired peaks: 2573 INFO @ Sun, 21 Jun 2020 20:56:39: start model_add_line... INFO @ Sun, 21 Jun 2020 20:56:39: start X-correlation... INFO @ Sun, 21 Jun 2020 20:56:39: end of X-cor INFO @ Sun, 21 Jun 2020 20:56:39: #2 finished! INFO @ Sun, 21 Jun 2020 20:56:39: #2 predicted fragment length is 241 bps INFO @ Sun, 21 Jun 2020 20:56:39: #2 alternative fragment length(s) may be 241 bps INFO @ Sun, 21 Jun 2020 20:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.05_model.r WARNING @ Sun, 21 Jun 2020 20:56:39: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:56:39: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Sun, 21 Jun 2020 20:56:39: #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 20:56:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:56:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:56:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:56:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:56:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.05_summits.bed INFO @ Sun, 21 Jun 2020 20:56:46: Done! pass1 - making usageList (493 chroms): 1 millis pass2 - checking and writing primary data (1204 records, 4 fields): 13 millis CompletedMACS2peakCalling 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 20:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.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 20:56:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:56:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:02: 1000000 INFO @ Sun, 21 Jun 2020 20:57:09: #1 tag size is determined as 250 bps INFO @ Sun, 21 Jun 2020 20:57:09: #1 tag size = 250 INFO @ Sun, 21 Jun 2020 20:57:09: #1 total tags in treatment: 1525058 INFO @ Sun, 21 Jun 2020 20:57:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:57:09: #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 20:57:09: #1 tags after filtering in treatment: 1524795 INFO @ Sun, 21 Jun 2020 20:57:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:57:09: #1 finished! INFO @ Sun, 21 Jun 2020 20:57:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:57:09: #2 number of paired peaks: 2573 INFO @ Sun, 21 Jun 2020 20:57:09: start model_add_line... INFO @ Sun, 21 Jun 2020 20:57:09: start X-correlation... INFO @ Sun, 21 Jun 2020 20:57:09: end of X-cor INFO @ Sun, 21 Jun 2020 20:57:09: #2 finished! INFO @ Sun, 21 Jun 2020 20:57:09: #2 predicted fragment length is 241 bps INFO @ Sun, 21 Jun 2020 20:57:09: #2 alternative fragment length(s) may be 241 bps INFO @ Sun, 21 Jun 2020 20:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.10_model.r WARNING @ Sun, 21 Jun 2020 20:57:09: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:57:09: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Sun, 21 Jun 2020 20:57:09: #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 20:57:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:57:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.10_summits.bed INFO @ Sun, 21 Jun 2020 20:57:15: Done! pass1 - making usageList (357 chroms): 1 millis pass2 - checking and writing primary data (689 records, 4 fields): 23 millis CompletedMACS2peakCalling 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 20:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.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 20:57:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:31: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:57:38: #1 tag size is determined as 250 bps INFO @ Sun, 21 Jun 2020 20:57:38: #1 tag size = 250 INFO @ Sun, 21 Jun 2020 20:57:38: #1 total tags in treatment: 1525058 INFO @ Sun, 21 Jun 2020 20:57:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:57:38: #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 20:57:38: #1 tags after filtering in treatment: 1524795 INFO @ Sun, 21 Jun 2020 20:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:57:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:57:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:57:38: #2 number of paired peaks: 2573 INFO @ Sun, 21 Jun 2020 20:57:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:57:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:57:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:57:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:57:38: #2 predicted fragment length is 241 bps INFO @ Sun, 21 Jun 2020 20:57:38: #2 alternative fragment length(s) may be 241 bps INFO @ Sun, 21 Jun 2020 20:57:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.20_model.r WARNING @ Sun, 21 Jun 2020 20:57:38: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:57:38: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Sun, 21 Jun 2020 20:57:38: #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 20:57:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:57:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:57:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:57:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:57:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:57:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3293410/SRX3293410.20_summits.bed INFO @ Sun, 21 Jun 2020 20:57:45: Done! pass1 - making usageList (244 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 7 millis CompletedMACS2peakCalling