Job ID = 6626551 SRX = SRX6813088 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13662810 spots for SRR10080054/SRR10080054.sra Written 13662810 spots for SRR10080054/SRR10080054.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626682 ("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: 00:03:09 13662810 reads; of these: 13662810 (100.00%) were unpaired; of these: 2927378 (21.43%) aligned 0 times 9253651 (67.73%) aligned exactly 1 time 1481781 (10.85%) aligned >1 times 78.57% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1566126 / 10735432 = 0.1459 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 @ Tue, 14 Jul 2020 07:36:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.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, 14 Jul 2020 07:36:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:40: 1000000 INFO @ Tue, 14 Jul 2020 07:36:45: 2000000 INFO @ Tue, 14 Jul 2020 07:36:50: 3000000 INFO @ Tue, 14 Jul 2020 07:36:55: 4000000 INFO @ Tue, 14 Jul 2020 07:37:00: 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 @ Tue, 14 Jul 2020 07:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.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, 14 Jul 2020 07:37:04: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:37:04: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:37:05: 6000000 INFO @ Tue, 14 Jul 2020 07:37:10: 1000000 INFO @ Tue, 14 Jul 2020 07:37:10: 7000000 INFO @ Tue, 14 Jul 2020 07:37:15: 2000000 INFO @ Tue, 14 Jul 2020 07:37:16: 8000000 INFO @ Tue, 14 Jul 2020 07:37:20: 3000000 INFO @ Tue, 14 Jul 2020 07:37:21: 9000000 INFO @ Tue, 14 Jul 2020 07:37:22: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:37:22: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:37:22: #1 total tags in treatment: 9169306 INFO @ Tue, 14 Jul 2020 07:37:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:37:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:37:22: #1 tags after filtering in treatment: 9169306 INFO @ Tue, 14 Jul 2020 07:37:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:37:22: #1 finished! INFO @ Tue, 14 Jul 2020 07:37:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:37:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:37:23: #2 number of paired peaks: 7683 INFO @ Tue, 14 Jul 2020 07:37:23: start model_add_line... INFO @ Tue, 14 Jul 2020 07:37:23: start X-correlation... INFO @ Tue, 14 Jul 2020 07:37:23: end of X-cor INFO @ Tue, 14 Jul 2020 07:37:23: #2 finished! INFO @ Tue, 14 Jul 2020 07:37:23: #2 predicted fragment length is 222 bps INFO @ Tue, 14 Jul 2020 07:37:23: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 14 Jul 2020 07:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.05_model.r INFO @ Tue, 14 Jul 2020 07:37:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:37:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:37:25: 4000000 INFO @ Tue, 14 Jul 2020 07:37:30: 5000000 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 @ Tue, 14 Jul 2020 07:37:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.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, 14 Jul 2020 07:37:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:37:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:37:34: 6000000 INFO @ Tue, 14 Jul 2020 07:37:39: 1000000 INFO @ Tue, 14 Jul 2020 07:37:39: 7000000 INFO @ Tue, 14 Jul 2020 07:37:44: 2000000 INFO @ Tue, 14 Jul 2020 07:37:44: 8000000 INFO @ Tue, 14 Jul 2020 07:37:49: 3000000 INFO @ Tue, 14 Jul 2020 07:37:49: 9000000 INFO @ Tue, 14 Jul 2020 07:37:50: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:37:50: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:37:50: #1 total tags in treatment: 9169306 INFO @ Tue, 14 Jul 2020 07:37:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:37:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:37:50: #1 tags after filtering in treatment: 9169306 INFO @ Tue, 14 Jul 2020 07:37:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:37:50: #1 finished! INFO @ Tue, 14 Jul 2020 07:37:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:37:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:37:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:51: #2 number of paired peaks: 7683 INFO @ Tue, 14 Jul 2020 07:37:51: start model_add_line... INFO @ Tue, 14 Jul 2020 07:37:52: start X-correlation... INFO @ Tue, 14 Jul 2020 07:37:52: end of X-cor INFO @ Tue, 14 Jul 2020 07:37:52: #2 finished! INFO @ Tue, 14 Jul 2020 07:37:52: #2 predicted fragment length is 222 bps INFO @ Tue, 14 Jul 2020 07:37:52: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 14 Jul 2020 07:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.10_model.r INFO @ Tue, 14 Jul 2020 07:37:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:37:54: 4000000 INFO @ Tue, 14 Jul 2020 07:37:59: 5000000 INFO @ Tue, 14 Jul 2020 07:38:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:38:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:38:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.05_summits.bed INFO @ Tue, 14 Jul 2020 07:38:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3942 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:38:04: 6000000 INFO @ Tue, 14 Jul 2020 07:38:09: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:38:14: 8000000 INFO @ Tue, 14 Jul 2020 07:38:18: 9000000 INFO @ Tue, 14 Jul 2020 07:38:19: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:38:19: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:38:19: #1 total tags in treatment: 9169306 INFO @ Tue, 14 Jul 2020 07:38:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:38:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:38:19: #1 tags after filtering in treatment: 9169306 INFO @ Tue, 14 Jul 2020 07:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:38:19: #1 finished! INFO @ Tue, 14 Jul 2020 07:38:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:38:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:38:20: #2 number of paired peaks: 7683 INFO @ Tue, 14 Jul 2020 07:38:20: start model_add_line... INFO @ Tue, 14 Jul 2020 07:38:21: start X-correlation... INFO @ Tue, 14 Jul 2020 07:38:21: end of X-cor INFO @ Tue, 14 Jul 2020 07:38:21: #2 finished! INFO @ Tue, 14 Jul 2020 07:38:21: #2 predicted fragment length is 222 bps INFO @ Tue, 14 Jul 2020 07:38:21: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 14 Jul 2020 07:38:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.20_model.r INFO @ Tue, 14 Jul 2020 07:38:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:38:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.10_summits.bed INFO @ Tue, 14 Jul 2020 07:38:30: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1780 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:38:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:38:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:38:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:38:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813088/SRX6813088.20_summits.bed INFO @ Tue, 14 Jul 2020 07:38:58: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (650 records, 4 fields): 48 millis CompletedMACS2peakCalling