Job ID = 16439302 SRX = SRX15206484 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:51:20 prefetch.2.10.7: 1) Downloading 'SRR19139319'... 2022-08-02T05:51:20 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:51:38 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:51:38 prefetch.2.10.7: 'SRR19139319' is valid 2022-08-02T05:51:38 prefetch.2.10.7: 1) 'SRR19139319' was downloaded successfully 2022-08-02T05:51:38 prefetch.2.10.7: 'SRR19139319' has 0 unresolved dependencies Read 8930128 spots for SRR19139319/SRR19139319.sra Written 8930128 spots for SRR19139319/SRR19139319.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439381 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:51 8930128 reads; of these: 8930128 (100.00%) were unpaired; of these: 140198 (1.57%) aligned 0 times 3277946 (36.71%) aligned exactly 1 time 5511984 (61.72%) aligned >1 times 98.43% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 894244 / 8789930 = 0.1017 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.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 @ Tue, 02 Aug 2022 15:02:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:02:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:03:09: 1000000 INFO @ Tue, 02 Aug 2022 15:03:19: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:03:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.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 @ Tue, 02 Aug 2022 15:03:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:03:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:03:29: 3000000 INFO @ Tue, 02 Aug 2022 15:03:38: 4000000 INFO @ Tue, 02 Aug 2022 15:03:42: 1000000 INFO @ Tue, 02 Aug 2022 15:03:47: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:03:55: 2000000 INFO @ Tue, 02 Aug 2022 15:03:56: 6000000 INFO @ Tue, 02 Aug 2022 15:03:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.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 @ Tue, 02 Aug 2022 15:03:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:03:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:04:06: 7000000 INFO @ Tue, 02 Aug 2022 15:04:08: 1000000 INFO @ Tue, 02 Aug 2022 15:04:10: 3000000 INFO @ Tue, 02 Aug 2022 15:04:15: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:04:15: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:04:15: #1 total tags in treatment: 7895686 INFO @ Tue, 02 Aug 2022 15:04:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:04:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:04:15: #1 tags after filtering in treatment: 7895686 INFO @ Tue, 02 Aug 2022 15:04:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:04:15: #1 finished! INFO @ Tue, 02 Aug 2022 15:04:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:04:16: #2 number of paired peaks: 3802 INFO @ Tue, 02 Aug 2022 15:04:16: start model_add_line... INFO @ Tue, 02 Aug 2022 15:04:16: start X-correlation... INFO @ Tue, 02 Aug 2022 15:04:16: end of X-cor INFO @ Tue, 02 Aug 2022 15:04:16: #2 finished! INFO @ Tue, 02 Aug 2022 15:04:16: #2 predicted fragment length is 158 bps INFO @ Tue, 02 Aug 2022 15:04:16: #2 alternative fragment length(s) may be 4,158 bps INFO @ Tue, 02 Aug 2022 15:04:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.05_model.r INFO @ Tue, 02 Aug 2022 15:04:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:04:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:04:19: 2000000 INFO @ Tue, 02 Aug 2022 15:04:24: 4000000 INFO @ Tue, 02 Aug 2022 15:04:29: 3000000 INFO @ Tue, 02 Aug 2022 15:04:38: 5000000 INFO @ Tue, 02 Aug 2022 15:04:40: 4000000 INFO @ Tue, 02 Aug 2022 15:04:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:04:51: 5000000 INFO @ Tue, 02 Aug 2022 15:04:52: 6000000 INFO @ Tue, 02 Aug 2022 15:05:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:05:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:05:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.05_summits.bed INFO @ Tue, 02 Aug 2022 15:05:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6715 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:05:01: 6000000 INFO @ Tue, 02 Aug 2022 15:05:06: 7000000 INFO @ Tue, 02 Aug 2022 15:05:12: 7000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:05:19: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:05:19: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:05:19: #1 total tags in treatment: 7895686 INFO @ Tue, 02 Aug 2022 15:05:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:05:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:05:19: #1 tags after filtering in treatment: 7895686 INFO @ Tue, 02 Aug 2022 15:05:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:05:19: #1 finished! INFO @ Tue, 02 Aug 2022 15:05:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:05:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:05:20: #2 number of paired peaks: 3802 INFO @ Tue, 02 Aug 2022 15:05:20: start model_add_line... INFO @ Tue, 02 Aug 2022 15:05:20: start X-correlation... INFO @ Tue, 02 Aug 2022 15:05:20: end of X-cor INFO @ Tue, 02 Aug 2022 15:05:20: #2 finished! INFO @ Tue, 02 Aug 2022 15:05:20: #2 predicted fragment length is 158 bps INFO @ Tue, 02 Aug 2022 15:05:20: #2 alternative fragment length(s) may be 4,158 bps INFO @ Tue, 02 Aug 2022 15:05:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.10_model.r INFO @ Tue, 02 Aug 2022 15:05:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:05:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:05:22: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:05:22: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:05:22: #1 total tags in treatment: 7895686 INFO @ Tue, 02 Aug 2022 15:05:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:05:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:05:22: #1 tags after filtering in treatment: 7895686 INFO @ Tue, 02 Aug 2022 15:05:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:05:22: #1 finished! INFO @ Tue, 02 Aug 2022 15:05:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:05:23: #2 number of paired peaks: 3802 INFO @ Tue, 02 Aug 2022 15:05:23: start model_add_line... INFO @ Tue, 02 Aug 2022 15:05:23: start X-correlation... INFO @ Tue, 02 Aug 2022 15:05:23: end of X-cor INFO @ Tue, 02 Aug 2022 15:05:23: #2 finished! INFO @ Tue, 02 Aug 2022 15:05:23: #2 predicted fragment length is 158 bps INFO @ Tue, 02 Aug 2022 15:05:23: #2 alternative fragment length(s) may be 4,158 bps INFO @ Tue, 02 Aug 2022 15:05:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.20_model.r INFO @ Tue, 02 Aug 2022 15:05:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:05:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:05:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:05:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:06:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:06:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.10_summits.bed INFO @ Tue, 02 Aug 2022 15:06:01: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2831 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:06:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:06:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:06:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206484/SRX15206484.20_summits.bed INFO @ Tue, 02 Aug 2022 15:06:03: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (887 records, 4 fields): 18 millis CompletedMACS2peakCalling