Job ID = 6455318 SRX = SRX287691 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:57:55 prefetch.2.10.7: 1) Downloading 'SRR869879'... 2020-06-21T09:57:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:00:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:00:15 prefetch.2.10.7: 'SRR869879' is valid 2020-06-21T10:00:15 prefetch.2.10.7: 1) 'SRR869879' was downloaded successfully Read 12249643 spots for SRR869879/SRR869879.sra Written 12249643 spots for SRR869879/SRR869879.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: 00:04:37 12249643 reads; of these: 12249643 (100.00%) were unpaired; of these: 681195 (5.56%) aligned 0 times 5381149 (43.93%) aligned exactly 1 time 6187299 (50.51%) aligned >1 times 94.44% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 2882114 / 11568448 = 0.2491 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 19:08:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.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 19:08:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:40: 1000000 INFO @ Sun, 21 Jun 2020 19:08:46: 2000000 INFO @ Sun, 21 Jun 2020 19:08:51: 3000000 INFO @ Sun, 21 Jun 2020 19:08:56: 4000000 INFO @ Sun, 21 Jun 2020 19:09:01: 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 19:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.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 19:09:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:07: 6000000 INFO @ Sun, 21 Jun 2020 19:09:11: 1000000 INFO @ Sun, 21 Jun 2020 19:09:13: 7000000 INFO @ Sun, 21 Jun 2020 19:09:17: 2000000 INFO @ Sun, 21 Jun 2020 19:09:19: 8000000 INFO @ Sun, 21 Jun 2020 19:09:23: 3000000 INFO @ Sun, 21 Jun 2020 19:09:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:23: #1 total tags in treatment: 8686334 INFO @ Sun, 21 Jun 2020 19:09:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:23: #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 19:09:24: #1 tags after filtering in treatment: 8686334 INFO @ Sun, 21 Jun 2020 19:09:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:25: #2 number of paired peaks: 2163 INFO @ Sun, 21 Jun 2020 19:09:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:25: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:09:25: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 19:09:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.05_model.r WARNING @ Sun, 21 Jun 2020 19:09:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:25: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 19:09:25: #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 19:09:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:29: 4000000 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 19:09:34: 5000000 INFO @ Sun, 21 Jun 2020 19:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.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 19:09:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:40: 6000000 INFO @ Sun, 21 Jun 2020 19:09:41: 1000000 INFO @ Sun, 21 Jun 2020 19:09:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:46: 7000000 INFO @ Sun, 21 Jun 2020 19:09:47: 2000000 INFO @ Sun, 21 Jun 2020 19:09:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.05_summits.bed INFO @ Sun, 21 Jun 2020 19:09:50: Done! pass1 - making usageList (921 chroms): 1 millis pass2 - checking and writing primary data (3887 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:52: 8000000 INFO @ Sun, 21 Jun 2020 19:09:53: 3000000 INFO @ Sun, 21 Jun 2020 19:09:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:56: #1 total tags in treatment: 8686334 INFO @ Sun, 21 Jun 2020 19:09:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:56: #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 19:09:57: #1 tags after filtering in treatment: 8686334 INFO @ Sun, 21 Jun 2020 19:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:57: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:57: #2 number of paired peaks: 2163 INFO @ Sun, 21 Jun 2020 19:09:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:58: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:58: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:09:58: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 19:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.10_model.r WARNING @ Sun, 21 Jun 2020 19:09:58: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:58: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 19:09:58: #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 19:09:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:59: 4000000 INFO @ Sun, 21 Jun 2020 19:10:04: 5000000 INFO @ Sun, 21 Jun 2020 19:10:10: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:10:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:16: 7000000 INFO @ Sun, 21 Jun 2020 19:10:21: 8000000 INFO @ Sun, 21 Jun 2020 19:10:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.10_summits.bed INFO @ Sun, 21 Jun 2020 19:10:23: Done! pass1 - making usageList (780 chroms): 2 millis pass2 - checking and writing primary data (2884 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:10:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:25: #1 total tags in treatment: 8686334 INFO @ Sun, 21 Jun 2020 19:10:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:25: #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 19:10:26: #1 tags after filtering in treatment: 8686334 INFO @ Sun, 21 Jun 2020 19:10:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:26: #2 number of paired peaks: 2163 INFO @ Sun, 21 Jun 2020 19:10:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:26: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:10:26: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 19:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.20_model.r WARNING @ Sun, 21 Jun 2020 19:10:26: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:26: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 19:10:26: #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 19:10:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287691/SRX287691.20_summits.bed INFO @ Sun, 21 Jun 2020 19:10:51: Done! pass1 - making usageList (518 chroms): 2 millis pass2 - checking and writing primary data (1194 records, 4 fields): 13 millis CompletedMACS2peakCalling