Job ID = 6454885 SRX = SRX2592473 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:28:59 prefetch.2.10.7: 1) Downloading 'SRR5289750'... 2020-06-21T09:28:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:32:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:32:02 prefetch.2.10.7: 'SRR5289750' is valid 2020-06-21T09:32:02 prefetch.2.10.7: 1) 'SRR5289750' was downloaded successfully Read 15466935 spots for SRR5289750/SRR5289750.sra Written 15466935 spots for SRR5289750/SRR5289750.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: 00:03:02 15466935 reads; of these: 15466935 (100.00%) were unpaired; of these: 4730517 (30.58%) aligned 0 times 8710743 (56.32%) aligned exactly 1 time 2025675 (13.10%) aligned >1 times 69.42% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 2988104 / 10736418 = 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 18:38:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.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 18:38:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:50: 1000000 INFO @ Sun, 21 Jun 2020 18:38:56: 2000000 INFO @ Sun, 21 Jun 2020 18:39:01: 3000000 INFO @ Sun, 21 Jun 2020 18:39:07: 4000000 INFO @ Sun, 21 Jun 2020 18:39:12: 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 18:39:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.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 18:39:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:18: 6000000 INFO @ Sun, 21 Jun 2020 18:39:21: 1000000 INFO @ Sun, 21 Jun 2020 18:39:24: 7000000 INFO @ Sun, 21 Jun 2020 18:39:27: 2000000 INFO @ Sun, 21 Jun 2020 18:39:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:39:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:39:29: #1 total tags in treatment: 7748314 INFO @ Sun, 21 Jun 2020 18:39:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:29: #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 18:39:29: #1 tags after filtering in treatment: 7748076 INFO @ Sun, 21 Jun 2020 18:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:29: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:30: #2 number of paired peaks: 7850 INFO @ Sun, 21 Jun 2020 18:39:30: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:31: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 18:39:31: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 18:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.05_model.r INFO @ Sun, 21 Jun 2020 18:39:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:32: 3000000 INFO @ Sun, 21 Jun 2020 18:39:38: 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 18:39:44: 5000000 INFO @ Sun, 21 Jun 2020 18:39:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.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 18:39:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:50: 6000000 INFO @ Sun, 21 Jun 2020 18:39:51: 1000000 INFO @ Sun, 21 Jun 2020 18:39:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:56: 7000000 INFO @ Sun, 21 Jun 2020 18:39:57: 2000000 INFO @ Sun, 21 Jun 2020 18:40:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:01: #1 total tags in treatment: 7748314 INFO @ Sun, 21 Jun 2020 18:40:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:01: #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 18:40:02: #1 tags after filtering in treatment: 7748076 INFO @ Sun, 21 Jun 2020 18:40:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:03: #2 number of paired peaks: 7850 INFO @ Sun, 21 Jun 2020 18:40:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:03: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 18:40:03: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 18:40:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.10_model.r INFO @ Sun, 21 Jun 2020 18:40:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:03: 3000000 INFO @ Sun, 21 Jun 2020 18:40:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.05_summits.bed INFO @ Sun, 21 Jun 2020 18:40:06: Done! pass1 - making usageList (180 chroms): 2 millis pass2 - checking and writing primary data (8426 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:09: 4000000 INFO @ Sun, 21 Jun 2020 18:40:14: 5000000 INFO @ Sun, 21 Jun 2020 18:40:20: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:40:26: 7000000 INFO @ Sun, 21 Jun 2020 18:40:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:40:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:40:30: #1 total tags in treatment: 7748314 INFO @ Sun, 21 Jun 2020 18:40:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:30: #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 18:40:31: #1 tags after filtering in treatment: 7748076 INFO @ Sun, 21 Jun 2020 18:40:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:32: #2 number of paired peaks: 7850 INFO @ Sun, 21 Jun 2020 18:40:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:32: #2 predicted fragment length is 198 bps INFO @ Sun, 21 Jun 2020 18:40:32: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 21 Jun 2020 18:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.20_model.r INFO @ Sun, 21 Jun 2020 18:40:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:40:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.10_summits.bed INFO @ Sun, 21 Jun 2020 18:40:37: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (6678 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592473/SRX2592473.20_summits.bed INFO @ Sun, 21 Jun 2020 18:41:06: Done! pass1 - making usageList (95 chroms): 2 millis pass2 - checking and writing primary data (4959 records, 4 fields): 9 millis CompletedMACS2peakCalling