Job ID = 6453864 SRX = SRX1531768 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:13:25 prefetch.2.10.7: 1) Downloading 'SRR3102826'... 2020-06-21T09:13:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:15:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:15:21 prefetch.2.10.7: 'SRR3102826' is valid 2020-06-21T09:15:21 prefetch.2.10.7: 1) 'SRR3102826' was downloaded successfully Read 11496479 spots for SRR3102826/SRR3102826.sra Written 11496479 spots for SRR3102826/SRR3102826.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: 00:02:28 11496479 reads; of these: 11496479 (100.00%) were unpaired; of these: 3131718 (27.24%) aligned 0 times 7235208 (62.93%) aligned exactly 1 time 1129553 (9.83%) aligned >1 times 72.76% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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_rmdupse_core] 3191074 / 8364761 = 0.3815 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 18:21:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.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 18:21:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:21:51: 1000000 INFO @ Sun, 21 Jun 2020 18:21:57: 2000000 INFO @ Sun, 21 Jun 2020 18:22:04: 3000000 INFO @ Sun, 21 Jun 2020 18:22:10: 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 18:22:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.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 18:22:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:17: 5000000 INFO @ Sun, 21 Jun 2020 18:22:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:22:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:22:19: #1 total tags in treatment: 5173687 INFO @ Sun, 21 Jun 2020 18:22:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:19: #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 18:22:19: #1 tags after filtering in treatment: 5173635 INFO @ Sun, 21 Jun 2020 18:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:20: #2 number of paired peaks: 2119 INFO @ Sun, 21 Jun 2020 18:22:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:20: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 18:22:20: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 18:22:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.05_model.r INFO @ Sun, 21 Jun 2020 18:22:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:20: 1000000 INFO @ Sun, 21 Jun 2020 18:22:27: 2000000 INFO @ Sun, 21 Jun 2020 18:22:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:33: 3000000 INFO @ Sun, 21 Jun 2020 18:22:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.05_summits.bed INFO @ Sun, 21 Jun 2020 18:22:39: Done! pass1 - making usageList (408 chroms): 2 millis pass2 - checking and writing primary data (6511 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:22:40: 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 18:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.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 18:22:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:47: 5000000 INFO @ Sun, 21 Jun 2020 18:22:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:22:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:22:49: #1 total tags in treatment: 5173687 INFO @ Sun, 21 Jun 2020 18:22:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:49: #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 18:22:50: #1 tags after filtering in treatment: 5173635 INFO @ Sun, 21 Jun 2020 18:22:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:50: 1000000 INFO @ Sun, 21 Jun 2020 18:22:50: #2 number of paired peaks: 2119 INFO @ Sun, 21 Jun 2020 18:22:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:50: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 18:22:50: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 18:22:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.10_model.r INFO @ Sun, 21 Jun 2020 18:22:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:22:57: 2000000 INFO @ Sun, 21 Jun 2020 18:23:03: 3000000 INFO @ Sun, 21 Jun 2020 18:23:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:09: 4000000 INFO @ Sun, 21 Jun 2020 18:23:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.10_summits.bed INFO @ Sun, 21 Jun 2020 18:23:10: Done! pass1 - making usageList (299 chroms): 2 millis pass2 - checking and writing primary data (3190 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:23:16: 5000000 INFO @ Sun, 21 Jun 2020 18:23:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:23:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:23:18: #1 total tags in treatment: 5173687 INFO @ Sun, 21 Jun 2020 18:23:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:18: #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 18:23:18: #1 tags after filtering in treatment: 5173635 INFO @ Sun, 21 Jun 2020 18:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:19: #2 number of paired peaks: 2119 INFO @ Sun, 21 Jun 2020 18:23:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:19: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 18:23:19: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 18:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.20_model.r INFO @ Sun, 21 Jun 2020 18:23:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:23:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531768/SRX1531768.20_summits.bed INFO @ Sun, 21 Jun 2020 18:23:38: Done! pass1 - making usageList (121 chroms): 1 millis pass2 - checking and writing primary data (1234 records, 4 fields): 9 millis CompletedMACS2peakCalling