Job ID = 6457113 SRX = SRX4375870 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:36:40 prefetch.2.10.7: 1) Downloading 'SRR7506524'... 2020-06-21T11:36:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:38:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:38:03 prefetch.2.10.7: 'SRR7506524' is valid 2020-06-21T11:38:03 prefetch.2.10.7: 1) 'SRR7506524' was downloaded successfully Read 7891197 spots for SRR7506524/SRR7506524.sra Written 7891197 spots for SRR7506524/SRR7506524.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: 00:01:56 7891197 reads; of these: 7891197 (100.00%) were unpaired; of these: 1343352 (17.02%) aligned 0 times 4944204 (62.65%) aligned exactly 1 time 1603641 (20.32%) aligned >1 times 82.98% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 1130442 / 6547845 = 0.1726 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 20:42:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.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 20:42:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:57: 1000000 INFO @ Sun, 21 Jun 2020 20:43:03: 2000000 INFO @ Sun, 21 Jun 2020 20:43:10: 3000000 INFO @ Sun, 21 Jun 2020 20:43:17: 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 20:43:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.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 20:43:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:25: 5000000 INFO @ Sun, 21 Jun 2020 20:43:28: 1000000 INFO @ Sun, 21 Jun 2020 20:43:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:28: #1 total tags in treatment: 5417403 INFO @ Sun, 21 Jun 2020 20:43:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:28: #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 20:43:28: #1 tags after filtering in treatment: 5417244 INFO @ Sun, 21 Jun 2020 20:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:29: #2 number of paired peaks: 1487 INFO @ Sun, 21 Jun 2020 20:43:29: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:29: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 20:43:29: #2 alternative fragment length(s) may be 218 bps INFO @ Sun, 21 Jun 2020 20:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.05_model.r INFO @ Sun, 21 Jun 2020 20:43:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:35: 2000000 INFO @ Sun, 21 Jun 2020 20:43:42: 3000000 INFO @ Sun, 21 Jun 2020 20:43:44: #3 Call peaks for each chromosome... 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 20:43:50: 4000000 INFO @ Sun, 21 Jun 2020 20:43:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.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 20:43:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.05_summits.bed INFO @ Sun, 21 Jun 2020 20:43:52: Done! pass1 - making usageList (649 chroms): 2 millis pass2 - checking and writing primary data (3634 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:58: 5000000 INFO @ Sun, 21 Jun 2020 20:43:58: 1000000 INFO @ Sun, 21 Jun 2020 20:44:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:44:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:44:01: #1 total tags in treatment: 5417403 INFO @ Sun, 21 Jun 2020 20:44:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:01: #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 20:44:01: #1 tags after filtering in treatment: 5417244 INFO @ Sun, 21 Jun 2020 20:44:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:02: #2 number of paired peaks: 1487 INFO @ Sun, 21 Jun 2020 20:44:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:02: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:02: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 20:44:02: #2 alternative fragment length(s) may be 218 bps INFO @ Sun, 21 Jun 2020 20:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.10_model.r INFO @ Sun, 21 Jun 2020 20:44:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:05: 2000000 INFO @ Sun, 21 Jun 2020 20:44:12: 3000000 INFO @ Sun, 21 Jun 2020 20:44:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:19: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:44:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.10_summits.bed INFO @ Sun, 21 Jun 2020 20:44:22: Done! pass1 - making usageList (479 chroms): 2 millis pass2 - checking and writing primary data (2125 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:25: 5000000 INFO @ Sun, 21 Jun 2020 20:44:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:44:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:44:28: #1 total tags in treatment: 5417403 INFO @ Sun, 21 Jun 2020 20:44:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:28: #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 20:44:29: #1 tags after filtering in treatment: 5417244 INFO @ Sun, 21 Jun 2020 20:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:29: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:29: #2 number of paired peaks: 1487 INFO @ Sun, 21 Jun 2020 20:44:29: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:29: #2 predicted fragment length is 218 bps INFO @ Sun, 21 Jun 2020 20:44:29: #2 alternative fragment length(s) may be 218 bps INFO @ Sun, 21 Jun 2020 20:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.20_model.r INFO @ Sun, 21 Jun 2020 20:44:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:44:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375870/SRX4375870.20_summits.bed INFO @ Sun, 21 Jun 2020 20:44:51: Done! pass1 - making usageList (260 chroms): 1 millis pass2 - checking and writing primary data (1120 records, 4 fields): 9 millis CompletedMACS2peakCalling