Job ID = 6457097 SRX = SRX4375857 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:40:28 prefetch.2.10.7: 1) Downloading 'SRR7506511'... 2020-06-21T11:40:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:42:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:42:59 prefetch.2.10.7: 'SRR7506511' is valid 2020-06-21T11:42:59 prefetch.2.10.7: 1) 'SRR7506511' was downloaded successfully Read 15466935 spots for SRR7506511/SRR7506511.sra Written 15466935 spots for SRR7506511/SRR7506511.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: 00:03:00 15466935 reads; of these: 15466935 (100.00%) were unpaired; of these: 4730512 (30.58%) aligned 0 times 8710690 (56.32%) aligned exactly 1 time 2025733 (13.10%) aligned >1 times 69.42% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 2987981 / 10736423 = 0.2783 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 20:49:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.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 20:49:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:49:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:49:47: 1000000 INFO @ Sun, 21 Jun 2020 20:49:54: 2000000 INFO @ Sun, 21 Jun 2020 20:50:00: 3000000 INFO @ Sun, 21 Jun 2020 20:50:07: 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 20:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.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 20:50:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:13: 5000000 INFO @ Sun, 21 Jun 2020 20:50:17: 1000000 INFO @ Sun, 21 Jun 2020 20:50:21: 6000000 INFO @ Sun, 21 Jun 2020 20:50:23: 2000000 INFO @ Sun, 21 Jun 2020 20:50:28: 7000000 INFO @ Sun, 21 Jun 2020 20:50:30: 3000000 INFO @ Sun, 21 Jun 2020 20:50:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:50:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:50:34: #1 total tags in treatment: 7748442 INFO @ Sun, 21 Jun 2020 20:50:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:50:34: #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 20:50:34: #1 tags after filtering in treatment: 7748221 INFO @ Sun, 21 Jun 2020 20:50:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:50:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:50:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:50:35: #2 number of paired peaks: 7833 INFO @ Sun, 21 Jun 2020 20:50:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:50:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:50:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:50:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:50:35: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 20:50:35: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 20:50:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.05_model.r INFO @ Sun, 21 Jun 2020 20:50:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:50:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:50:36: 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 20:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.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 20:50:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:42: 5000000 INFO @ Sun, 21 Jun 2020 20:50:47: 1000000 INFO @ Sun, 21 Jun 2020 20:50:49: 6000000 INFO @ Sun, 21 Jun 2020 20:50:55: 2000000 INFO @ Sun, 21 Jun 2020 20:50:56: 7000000 INFO @ Sun, 21 Jun 2020 20:50:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:51:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:51:01: #1 total tags in treatment: 7748442 INFO @ Sun, 21 Jun 2020 20:51:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:01: #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 20:51:01: #1 tags after filtering in treatment: 7748221 INFO @ Sun, 21 Jun 2020 20:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:02: 3000000 INFO @ Sun, 21 Jun 2020 20:51:02: #2 number of paired peaks: 7833 INFO @ Sun, 21 Jun 2020 20:51:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:03: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 20:51:03: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 20:51:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.10_model.r INFO @ Sun, 21 Jun 2020 20:51:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:08: 4000000 INFO @ Sun, 21 Jun 2020 20:51:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.05_summits.bed INFO @ Sun, 21 Jun 2020 20:51:09: Done! pass1 - making usageList (170 chroms): 2 millis pass2 - checking and writing primary data (8432 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:51:15: 5000000 INFO @ Sun, 21 Jun 2020 20:51:21: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:51:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:29: 7000000 INFO @ Sun, 21 Jun 2020 20:51:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:51:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:51:34: #1 total tags in treatment: 7748442 INFO @ Sun, 21 Jun 2020 20:51:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:34: #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 20:51:34: #1 tags after filtering in treatment: 7748221 INFO @ Sun, 21 Jun 2020 20:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:35: #2 number of paired peaks: 7833 INFO @ Sun, 21 Jun 2020 20:51:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:35: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 20:51:35: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 20:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.20_model.r INFO @ Sun, 21 Jun 2020 20:51:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.10_summits.bed INFO @ Sun, 21 Jun 2020 20:51:38: Done! pass1 - making usageList (130 chroms): 1 millis pass2 - checking and writing primary data (6671 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:51:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375857/SRX4375857.20_summits.bed INFO @ Sun, 21 Jun 2020 20:52:09: Done! pass1 - making usageList (92 chroms): 2 millis pass2 - checking and writing primary data (4955 records, 4 fields): 9 millis CompletedMACS2peakCalling