Job ID = 6626548 SRX = SRX6813085 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15652572 spots for SRR10080057/SRR10080057.sra Written 15652572 spots for SRR10080057/SRR10080057.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626677 ("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: 00:03:27 15652572 reads; of these: 15652572 (100.00%) were unpaired; of these: 7466631 (47.70%) aligned 0 times 6723679 (42.96%) aligned exactly 1 time 1462262 (9.34%) aligned >1 times 52.30% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 831508 / 8185941 = 0.1016 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 07:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.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 07:35:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:35:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:35:13: 1000000 INFO @ Tue, 14 Jul 2020 07:35:19: 2000000 INFO @ Tue, 14 Jul 2020 07:35:24: 3000000 INFO @ Tue, 14 Jul 2020 07:35:29: 4000000 INFO @ Tue, 14 Jul 2020 07:35:34: 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 07:35:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.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 07:35:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:35:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:35:39: 6000000 INFO @ Tue, 14 Jul 2020 07:35:44: 7000000 INFO @ Tue, 14 Jul 2020 07:35:44: 1000000 INFO @ Tue, 14 Jul 2020 07:35:46: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:35:46: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:35:46: #1 total tags in treatment: 7354433 INFO @ Tue, 14 Jul 2020 07:35:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:35:46: #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 07:35:46: #1 tags after filtering in treatment: 7354433 INFO @ Tue, 14 Jul 2020 07:35:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:35:46: #1 finished! INFO @ Tue, 14 Jul 2020 07:35:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:35:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:35:46: #2 number of paired peaks: 2493 INFO @ Tue, 14 Jul 2020 07:35:46: start model_add_line... INFO @ Tue, 14 Jul 2020 07:35:46: start X-correlation... INFO @ Tue, 14 Jul 2020 07:35:46: end of X-cor INFO @ Tue, 14 Jul 2020 07:35:46: #2 finished! INFO @ Tue, 14 Jul 2020 07:35:46: #2 predicted fragment length is 210 bps INFO @ Tue, 14 Jul 2020 07:35:46: #2 alternative fragment length(s) may be 210 bps INFO @ Tue, 14 Jul 2020 07:35:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.05_model.r INFO @ Tue, 14 Jul 2020 07:35:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:35:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:35:49: 2000000 INFO @ Tue, 14 Jul 2020 07:35:54: 3000000 INFO @ Tue, 14 Jul 2020 07:35:59: 4000000 INFO @ Tue, 14 Jul 2020 07:36:04: 5000000 INFO @ Tue, 14 Jul 2020 07:36:04: #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 @ Tue, 14 Jul 2020 07:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.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 07:36:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:10: 6000000 INFO @ Tue, 14 Jul 2020 07:36:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:36:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:36:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.05_summits.bed INFO @ Tue, 14 Jul 2020 07:36:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6180 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:36:14: 1000000 INFO @ Tue, 14 Jul 2020 07:36:15: 7000000 INFO @ Tue, 14 Jul 2020 07:36:17: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:36:17: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:36:17: #1 total tags in treatment: 7354433 INFO @ Tue, 14 Jul 2020 07:36:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:17: #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 07:36:17: #1 tags after filtering in treatment: 7354433 INFO @ Tue, 14 Jul 2020 07:36:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:36:17: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:18: #2 number of paired peaks: 2493 INFO @ Tue, 14 Jul 2020 07:36:18: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:18: #2 predicted fragment length is 210 bps INFO @ Tue, 14 Jul 2020 07:36:18: #2 alternative fragment length(s) may be 210 bps INFO @ Tue, 14 Jul 2020 07:36:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.10_model.r INFO @ Tue, 14 Jul 2020 07:36:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:36:20: 2000000 INFO @ Tue, 14 Jul 2020 07:36:26: 3000000 INFO @ Tue, 14 Jul 2020 07:36:32: 4000000 INFO @ Tue, 14 Jul 2020 07:36:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:36:38: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:36:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:36:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:36:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.10_summits.bed INFO @ Tue, 14 Jul 2020 07:36:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4831 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:36:43: 6000000 INFO @ Tue, 14 Jul 2020 07:36:49: 7000000 INFO @ Tue, 14 Jul 2020 07:36:51: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:36:51: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:36:51: #1 total tags in treatment: 7354433 INFO @ Tue, 14 Jul 2020 07:36:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:51: #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 07:36:51: #1 tags after filtering in treatment: 7354433 INFO @ Tue, 14 Jul 2020 07:36:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:36:51: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:52: #2 number of paired peaks: 2493 INFO @ Tue, 14 Jul 2020 07:36:52: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:52: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:52: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:52: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:52: #2 predicted fragment length is 210 bps INFO @ Tue, 14 Jul 2020 07:36:52: #2 alternative fragment length(s) may be 210 bps INFO @ Tue, 14 Jul 2020 07:36:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.20_model.r INFO @ Tue, 14 Jul 2020 07:36:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:37:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813085/SRX6813085.20_summits.bed INFO @ Tue, 14 Jul 2020 07:37:17: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3457 records, 4 fields): 5 millis CompletedMACS2peakCalling