Job ID = 6454627 SRX = SRX2422631 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:17:24 prefetch.2.10.7: 1) Downloading 'SRR5110245'... 2020-06-21T09:17:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:20:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:20:42 prefetch.2.10.7: 1) 'SRR5110245' was downloaded successfully Read 15442783 spots for SRR5110245/SRR5110245.sra Written 15442783 spots for SRR5110245/SRR5110245.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: 00:05:37 15442783 reads; of these: 15442783 (100.00%) were unpaired; of these: 641392 (4.15%) aligned 0 times 10217747 (66.17%) aligned exactly 1 time 4583644 (29.68%) aligned >1 times 95.85% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 1914530 / 14801391 = 0.1293 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 18:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.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 18:32:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:53: 1000000 INFO @ Sun, 21 Jun 2020 18:33:01: 2000000 INFO @ Sun, 21 Jun 2020 18:33:08: 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 18:33:15: 4000000 INFO @ Sun, 21 Jun 2020 18:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.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 18:33:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:23: 5000000 INFO @ Sun, 21 Jun 2020 18:33:25: 1000000 INFO @ Sun, 21 Jun 2020 18:33:30: 6000000 INFO @ Sun, 21 Jun 2020 18:33:33: 2000000 INFO @ Sun, 21 Jun 2020 18:33:37: 7000000 INFO @ Sun, 21 Jun 2020 18:33:42: 3000000 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 18:33:45: 8000000 INFO @ Sun, 21 Jun 2020 18:33:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.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 18:33:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:51: 4000000 INFO @ Sun, 21 Jun 2020 18:33:52: 9000000 INFO @ Sun, 21 Jun 2020 18:33:54: 1000000 INFO @ Sun, 21 Jun 2020 18:34:00: 5000000 INFO @ Sun, 21 Jun 2020 18:34:00: 10000000 INFO @ Sun, 21 Jun 2020 18:34:02: 2000000 INFO @ Sun, 21 Jun 2020 18:34:08: 6000000 INFO @ Sun, 21 Jun 2020 18:34:09: 11000000 INFO @ Sun, 21 Jun 2020 18:34:10: 3000000 INFO @ Sun, 21 Jun 2020 18:34:17: 12000000 INFO @ Sun, 21 Jun 2020 18:34:17: 7000000 INFO @ Sun, 21 Jun 2020 18:34:18: 4000000 INFO @ Sun, 21 Jun 2020 18:34:24: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:34:24: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:34:24: #1 total tags in treatment: 12886861 INFO @ Sun, 21 Jun 2020 18:34:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:24: #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 18:34:24: #1 tags after filtering in treatment: 12886759 INFO @ Sun, 21 Jun 2020 18:34:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:25: 8000000 INFO @ Sun, 21 Jun 2020 18:34:25: #2 number of paired peaks: 1581 INFO @ Sun, 21 Jun 2020 18:34:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:25: 5000000 INFO @ Sun, 21 Jun 2020 18:34:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:25: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 18:34:25: #2 alternative fragment length(s) may be 3,74 bps INFO @ Sun, 21 Jun 2020 18:34:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.05_model.r WARNING @ Sun, 21 Jun 2020 18:34:25: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:34:25: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Sun, 21 Jun 2020 18:34:25: #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 18:34:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:33: 6000000 INFO @ Sun, 21 Jun 2020 18:34:33: 9000000 INFO @ Sun, 21 Jun 2020 18:34:40: 7000000 INFO @ Sun, 21 Jun 2020 18:34:41: 10000000 INFO @ Sun, 21 Jun 2020 18:34:47: 8000000 INFO @ Sun, 21 Jun 2020 18:34:49: 11000000 INFO @ Sun, 21 Jun 2020 18:34:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:54: 9000000 INFO @ Sun, 21 Jun 2020 18:34:58: 12000000 INFO @ Sun, 21 Jun 2020 18:35:01: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:35:05: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:35:05: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:35:05: #1 total tags in treatment: 12886861 INFO @ Sun, 21 Jun 2020 18:35:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:05: #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 18:35:06: #1 tags after filtering in treatment: 12886759 INFO @ Sun, 21 Jun 2020 18:35:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.05_summits.bed INFO @ Sun, 21 Jun 2020 18:35:06: Done! pass1 - making usageList (622 chroms): 1 millis pass2 - checking and writing primary data (3057 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:35:07: #2 number of paired peaks: 1581 INFO @ Sun, 21 Jun 2020 18:35:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:07: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 18:35:07: #2 alternative fragment length(s) may be 3,74 bps INFO @ Sun, 21 Jun 2020 18:35:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.10_model.r WARNING @ Sun, 21 Jun 2020 18:35:07: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:07: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Sun, 21 Jun 2020 18:35:07: #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 18:35:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:09: 11000000 INFO @ Sun, 21 Jun 2020 18:35:16: 12000000 INFO @ Sun, 21 Jun 2020 18:35:23: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:35:23: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:35:23: #1 total tags in treatment: 12886861 INFO @ Sun, 21 Jun 2020 18:35:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:23: #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 18:35:24: #1 tags after filtering in treatment: 12886759 INFO @ Sun, 21 Jun 2020 18:35:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:25: #2 number of paired peaks: 1581 INFO @ Sun, 21 Jun 2020 18:35:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:25: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 18:35:25: #2 alternative fragment length(s) may be 3,74 bps INFO @ Sun, 21 Jun 2020 18:35:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.20_model.r WARNING @ Sun, 21 Jun 2020 18:35:25: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:25: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Sun, 21 Jun 2020 18:35:25: #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 18:35:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.10_summits.bed INFO @ Sun, 21 Jun 2020 18:35:47: Done! pass1 - making usageList (499 chroms): 2 millis pass2 - checking and writing primary data (1763 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:35:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422631/SRX2422631.20_summits.bed INFO @ Sun, 21 Jun 2020 18:36:06: Done! pass1 - making usageList (335 chroms): 2 millis pass2 - checking and writing primary data (772 records, 4 fields): 19 millis CompletedMACS2peakCalling