Job ID = 6455299 SRX = SRX287676 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:58:56 prefetch.2.10.7: 1) Downloading 'SRR869864'... 2020-06-21T09:58:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:01:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:01:24 prefetch.2.10.7: 'SRR869864' is valid 2020-06-21T10:01:24 prefetch.2.10.7: 1) 'SRR869864' was downloaded successfully Read 14983362 spots for SRR869864/SRR869864.sra Written 14983362 spots for SRR869864/SRR869864.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: 00:07:08 14983362 reads; of these: 14983362 (100.00%) were unpaired; of these: 983211 (6.56%) aligned 0 times 2869722 (19.15%) aligned exactly 1 time 11130429 (74.29%) aligned >1 times 93.44% overall alignment rate Time searching: 00:07:08 Overall time: 00:07:08 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] 5575346 / 14000151 = 0.3982 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 19:12:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.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 19:12:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:48: 1000000 INFO @ Sun, 21 Jun 2020 19:12:54: 2000000 INFO @ Sun, 21 Jun 2020 19:13:00: 3000000 INFO @ Sun, 21 Jun 2020 19:13:07: 4000000 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 19:13:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.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 19:13:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:13: 5000000 INFO @ Sun, 21 Jun 2020 19:13:18: 1000000 INFO @ Sun, 21 Jun 2020 19:13:20: 6000000 INFO @ Sun, 21 Jun 2020 19:13:25: 2000000 INFO @ Sun, 21 Jun 2020 19:13:27: 7000000 INFO @ Sun, 21 Jun 2020 19:13:31: 3000000 INFO @ Sun, 21 Jun 2020 19:13:33: 8000000 INFO @ Sun, 21 Jun 2020 19:13:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:36: #1 total tags in treatment: 8424805 INFO @ Sun, 21 Jun 2020 19:13:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:36: #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 19:13:37: #1 tags after filtering in treatment: 8424804 INFO @ Sun, 21 Jun 2020 19:13:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:37: 4000000 INFO @ Sun, 21 Jun 2020 19:13:38: #2 number of paired peaks: 5191 INFO @ Sun, 21 Jun 2020 19:13:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:38: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:13:38: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 19:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.05_model.r WARNING @ Sun, 21 Jun 2020 19:13:38: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:38: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 19:13:38: #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 19:13:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:38: #3 Pre-compute pvalue-qvalue table... 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 19:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.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 19:13:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:43: 5000000 INFO @ Sun, 21 Jun 2020 19:13:49: 1000000 INFO @ Sun, 21 Jun 2020 19:13:50: 6000000 INFO @ Sun, 21 Jun 2020 19:13:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:55: 2000000 INFO @ Sun, 21 Jun 2020 19:13:57: 7000000 INFO @ Sun, 21 Jun 2020 19:14:02: 3000000 INFO @ Sun, 21 Jun 2020 19:14:03: 8000000 INFO @ Sun, 21 Jun 2020 19:14:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.05_summits.bed INFO @ Sun, 21 Jun 2020 19:14:05: Done! pass1 - making usageList (1334 chroms): 2 millis pass2 - checking and writing primary data (5404 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:06: #1 total tags in treatment: 8424805 INFO @ Sun, 21 Jun 2020 19:14:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:06: #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 19:14:07: #1 tags after filtering in treatment: 8424804 INFO @ Sun, 21 Jun 2020 19:14:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:08: #2 number of paired peaks: 5191 INFO @ Sun, 21 Jun 2020 19:14:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:08: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:14:08: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 19:14:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.10_model.r WARNING @ Sun, 21 Jun 2020 19:14:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:08: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 19:14:08: #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 19:14:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:09: 4000000 INFO @ Sun, 21 Jun 2020 19:14:15: 5000000 INFO @ Sun, 21 Jun 2020 19:14:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:14:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:28: 7000000 INFO @ Sun, 21 Jun 2020 19:14:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.10_summits.bed INFO @ Sun, 21 Jun 2020 19:14:34: Done! INFO @ Sun, 21 Jun 2020 19:14:35: 8000000 pass1 - making usageList (1045 chroms): 1 millis pass2 - checking and writing primary data (3389 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:38: #1 total tags in treatment: 8424805 INFO @ Sun, 21 Jun 2020 19:14:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:38: #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 19:14:38: #1 tags after filtering in treatment: 8424804 INFO @ Sun, 21 Jun 2020 19:14:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:39: #2 number of paired peaks: 5191 INFO @ Sun, 21 Jun 2020 19:14:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:39: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:14:39: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 19:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.20_model.r WARNING @ Sun, 21 Jun 2020 19:14:39: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:39: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 19:14:39: #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 19:14:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:14:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287676/SRX287676.20_summits.bed INFO @ Sun, 21 Jun 2020 19:15:07: Done! pass1 - making usageList (759 chroms): 1 millis pass2 - checking and writing primary data (2348 records, 4 fields): 24 millis CompletedMACS2peakCalling