Job ID = 6626544 SRX = SRX6813082 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13826361 spots for SRR10080060/SRR10080060.sra Written 13826361 spots for SRR10080060/SRR10080060.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626671 ("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: 00:03:21 13826361 reads; of these: 13826361 (100.00%) were unpaired; of these: 2227570 (16.11%) aligned 0 times 10003623 (72.35%) aligned exactly 1 time 1595168 (11.54%) aligned >1 times 83.89% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 2537164 / 11598791 = 0.2187 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 07:33:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.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 07:33:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:33:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:33:18: 1000000 INFO @ Tue, 14 Jul 2020 07:33:24: 2000000 INFO @ Tue, 14 Jul 2020 07:33:30: 3000000 INFO @ Tue, 14 Jul 2020 07:33:36: 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 @ Tue, 14 Jul 2020 07:33:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.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 07:33:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:33:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:33:42: 5000000 INFO @ Tue, 14 Jul 2020 07:33:49: 1000000 INFO @ Tue, 14 Jul 2020 07:33:49: 6000000 INFO @ Tue, 14 Jul 2020 07:33:55: 2000000 INFO @ Tue, 14 Jul 2020 07:33:56: 7000000 INFO @ Tue, 14 Jul 2020 07:34:02: 3000000 INFO @ Tue, 14 Jul 2020 07:34:02: 8000000 INFO @ Tue, 14 Jul 2020 07:34:09: 4000000 INFO @ Tue, 14 Jul 2020 07:34:09: 9000000 INFO @ Tue, 14 Jul 2020 07:34:10: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:34:10: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:34:10: #1 total tags in treatment: 9061627 INFO @ Tue, 14 Jul 2020 07:34:10: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:34:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Tue, 14 Jul 2020 07:34:10: #1 tags after filtering in treatment: 9061627 INFO @ Tue, 14 Jul 2020 07:34:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:34:10: #1 finished! INFO @ Tue, 14 Jul 2020 07:34:10: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:34:10: #2 looking for paired plus/minus strand peaks... 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 07:34:11: #2 number of paired peaks: 3944 INFO @ Tue, 14 Jul 2020 07:34:11: start model_add_line... INFO @ Tue, 14 Jul 2020 07:34:11: start X-correlation... INFO @ Tue, 14 Jul 2020 07:34:11: end of X-cor INFO @ Tue, 14 Jul 2020 07:34:11: #2 finished! INFO @ Tue, 14 Jul 2020 07:34:11: #2 predicted fragment length is 227 bps INFO @ Tue, 14 Jul 2020 07:34:11: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 14 Jul 2020 07:34:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.05_model.r INFO @ Tue, 14 Jul 2020 07:34:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:34:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:34:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.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 07:34:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:34:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:34:16: 5000000 INFO @ Tue, 14 Jul 2020 07:34:19: 1000000 INFO @ Tue, 14 Jul 2020 07:34:23: 6000000 INFO @ Tue, 14 Jul 2020 07:34:25: 2000000 INFO @ Tue, 14 Jul 2020 07:34:29: 7000000 INFO @ Tue, 14 Jul 2020 07:34:32: 3000000 INFO @ Tue, 14 Jul 2020 07:34:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:34:36: 8000000 INFO @ Tue, 14 Jul 2020 07:34:39: 4000000 INFO @ Tue, 14 Jul 2020 07:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.05_summits.bed INFO @ Tue, 14 Jul 2020 07:34:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7478 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:34:43: 9000000 INFO @ Tue, 14 Jul 2020 07:34:44: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:34:44: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:34:44: #1 total tags in treatment: 9061627 INFO @ Tue, 14 Jul 2020 07:34:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:34:44: #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 07:34:44: #1 tags after filtering in treatment: 9061627 INFO @ Tue, 14 Jul 2020 07:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:34:44: #1 finished! INFO @ Tue, 14 Jul 2020 07:34:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:34:45: #2 number of paired peaks: 3944 INFO @ Tue, 14 Jul 2020 07:34:45: start model_add_line... INFO @ Tue, 14 Jul 2020 07:34:45: start X-correlation... INFO @ Tue, 14 Jul 2020 07:34:45: end of X-cor INFO @ Tue, 14 Jul 2020 07:34:45: #2 finished! INFO @ Tue, 14 Jul 2020 07:34:45: #2 predicted fragment length is 227 bps INFO @ Tue, 14 Jul 2020 07:34:45: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 14 Jul 2020 07:34:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.10_model.r INFO @ Tue, 14 Jul 2020 07:34:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:34:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:34:46: 5000000 INFO @ Tue, 14 Jul 2020 07:34:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:34:59: 7000000 INFO @ Tue, 14 Jul 2020 07:35:05: 8000000 INFO @ Tue, 14 Jul 2020 07:35:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:35:11: 9000000 INFO @ Tue, 14 Jul 2020 07:35:12: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:35:12: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:35:12: #1 total tags in treatment: 9061627 INFO @ Tue, 14 Jul 2020 07:35:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:35:12: #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 07:35:12: #1 tags after filtering in treatment: 9061627 INFO @ Tue, 14 Jul 2020 07:35:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:35:12: #1 finished! INFO @ Tue, 14 Jul 2020 07:35:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:35:13: #2 number of paired peaks: 3944 INFO @ Tue, 14 Jul 2020 07:35:13: start model_add_line... INFO @ Tue, 14 Jul 2020 07:35:13: start X-correlation... INFO @ Tue, 14 Jul 2020 07:35:13: end of X-cor INFO @ Tue, 14 Jul 2020 07:35:13: #2 finished! INFO @ Tue, 14 Jul 2020 07:35:13: #2 predicted fragment length is 227 bps INFO @ Tue, 14 Jul 2020 07:35:13: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 14 Jul 2020 07:35:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.20_model.r INFO @ Tue, 14 Jul 2020 07:35:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:35:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.10_summits.bed INFO @ Tue, 14 Jul 2020 07:35:15: Done! BigWig に変換しました。 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6216 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:35:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:35:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:35:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:35:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813082/SRX6813082.20_summits.bed INFO @ Tue, 14 Jul 2020 07:35:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4887 records, 4 fields): 26 millis CompletedMACS2peakCalling