Job ID = 6456968 SRX = SRX4158200 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:20:12 prefetch.2.10.7: 1) Downloading 'SRR7253480'... 2020-06-21T11:20:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:25 prefetch.2.10.7: 1) 'SRR7253480' was downloaded successfully Read 21261146 spots for SRR7253480/SRR7253480.sra Written 21261146 spots for SRR7253480/SRR7253480.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:44 21261146 reads; of these: 21261146 (100.00%) were unpaired; of these: 666302 (3.13%) aligned 0 times 11808970 (55.54%) aligned exactly 1 time 8785874 (41.32%) aligned >1 times 96.87% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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 12 files... [bam_rmdupse_core] 3737488 / 20594844 = 0.1815 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 20:33:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.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 20:33:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:33:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:05: 1000000 INFO @ Sun, 21 Jun 2020 20:34:11: 2000000 INFO @ Sun, 21 Jun 2020 20:34:18: 3000000 INFO @ Sun, 21 Jun 2020 20:34:25: 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 20:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.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 20:34:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:32: 5000000 INFO @ Sun, 21 Jun 2020 20:34:35: 1000000 INFO @ Sun, 21 Jun 2020 20:34:39: 6000000 INFO @ Sun, 21 Jun 2020 20:34:42: 2000000 INFO @ Sun, 21 Jun 2020 20:34:46: 7000000 INFO @ Sun, 21 Jun 2020 20:34:49: 3000000 INFO @ Sun, 21 Jun 2020 20:34:53: 8000000 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 20:34:57: 4000000 INFO @ Sun, 21 Jun 2020 20:34:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.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 20:34:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:01: 9000000 INFO @ Sun, 21 Jun 2020 20:35:04: 5000000 INFO @ Sun, 21 Jun 2020 20:35:06: 1000000 INFO @ Sun, 21 Jun 2020 20:35:08: 10000000 INFO @ Sun, 21 Jun 2020 20:35:12: 6000000 INFO @ Sun, 21 Jun 2020 20:35:13: 2000000 INFO @ Sun, 21 Jun 2020 20:35:16: 11000000 INFO @ Sun, 21 Jun 2020 20:35:19: 7000000 INFO @ Sun, 21 Jun 2020 20:35:20: 3000000 INFO @ Sun, 21 Jun 2020 20:35:23: 12000000 INFO @ Sun, 21 Jun 2020 20:35:27: 8000000 INFO @ Sun, 21 Jun 2020 20:35:28: 4000000 INFO @ Sun, 21 Jun 2020 20:35:31: 13000000 INFO @ Sun, 21 Jun 2020 20:35:35: 9000000 INFO @ Sun, 21 Jun 2020 20:35:35: 5000000 INFO @ Sun, 21 Jun 2020 20:35:38: 14000000 INFO @ Sun, 21 Jun 2020 20:35:42: 10000000 INFO @ Sun, 21 Jun 2020 20:35:43: 6000000 INFO @ Sun, 21 Jun 2020 20:35:46: 15000000 INFO @ Sun, 21 Jun 2020 20:35:50: 11000000 INFO @ Sun, 21 Jun 2020 20:35:51: 7000000 INFO @ Sun, 21 Jun 2020 20:35:53: 16000000 INFO @ Sun, 21 Jun 2020 20:35:58: 12000000 INFO @ Sun, 21 Jun 2020 20:35:58: 8000000 INFO @ Sun, 21 Jun 2020 20:36:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:36:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:36:00: #1 total tags in treatment: 16857356 INFO @ Sun, 21 Jun 2020 20:36:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:00: #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 20:36:00: #1 tags after filtering in treatment: 16857307 INFO @ Sun, 21 Jun 2020 20:36:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:00: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:36:02: #2 number of paired peaks: 3619 INFO @ Sun, 21 Jun 2020 20:36:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:36:02: start X-correlation... INFO @ Sun, 21 Jun 2020 20:36:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:36:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:36:02: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 20:36:02: #2 alternative fragment length(s) may be 4,162 bps INFO @ Sun, 21 Jun 2020 20:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.05_model.r INFO @ Sun, 21 Jun 2020 20:36:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:36:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:36:06: 9000000 INFO @ Sun, 21 Jun 2020 20:36:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:36:13: 10000000 INFO @ Sun, 21 Jun 2020 20:36:14: 14000000 INFO @ Sun, 21 Jun 2020 20:36:21: 11000000 INFO @ Sun, 21 Jun 2020 20:36:21: 15000000 INFO @ Sun, 21 Jun 2020 20:36:28: 12000000 INFO @ Sun, 21 Jun 2020 20:36:29: 16000000 INFO @ Sun, 21 Jun 2020 20:36:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:36:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:36:36: #1 total tags in treatment: 16857356 INFO @ Sun, 21 Jun 2020 20:36:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:36: #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 20:36:36: 13000000 INFO @ Sun, 21 Jun 2020 20:36:36: #1 tags after filtering in treatment: 16857307 INFO @ Sun, 21 Jun 2020 20:36:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:36:38: #2 number of paired peaks: 3619 INFO @ Sun, 21 Jun 2020 20:36:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:36:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:36:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:36:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:36:38: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 20:36:38: #2 alternative fragment length(s) may be 4,162 bps INFO @ Sun, 21 Jun 2020 20:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.10_model.r INFO @ Sun, 21 Jun 2020 20:36:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:36:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:36:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:36:43: 14000000 INFO @ Sun, 21 Jun 2020 20:36:50: 15000000 INFO @ Sun, 21 Jun 2020 20:36:56: 16000000 INFO @ Sun, 21 Jun 2020 20:37:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.05_summits.bed INFO @ Sun, 21 Jun 2020 20:37:01: Done! pass1 - making usageList (769 chroms): 3 millis pass2 - checking and writing primary data (13044 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:37:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:37:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:37:03: #1 total tags in treatment: 16857356 INFO @ Sun, 21 Jun 2020 20:37:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:03: #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 20:37:03: #1 tags after filtering in treatment: 16857307 INFO @ Sun, 21 Jun 2020 20:37:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:03: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:04: #2 number of paired peaks: 3619 INFO @ Sun, 21 Jun 2020 20:37:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:05: #2 predicted fragment length is 162 bps INFO @ Sun, 21 Jun 2020 20:37:05: #2 alternative fragment length(s) may be 4,162 bps INFO @ Sun, 21 Jun 2020 20:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.20_model.r INFO @ Sun, 21 Jun 2020 20:37:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:37:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.10_summits.bed INFO @ Sun, 21 Jun 2020 20:37:38: Done! pass1 - making usageList (590 chroms): 2 millis pass2 - checking and writing primary data (7665 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:37:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158200/SRX4158200.20_summits.bed INFO @ Sun, 21 Jun 2020 20:38:04: Done! pass1 - making usageList (404 chroms): 1 millis pass2 - checking and writing primary data (2997 records, 4 fields): 15 millis CompletedMACS2peakCalling