Job ID = 6626547 SRX = SRX6813084 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16727871 spots for SRR10080058/SRR10080058.sra Written 16727871 spots for SRR10080058/SRR10080058.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626686 ("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: 00:04:45 16727871 reads; of these: 16727871 (100.00%) were unpaired; of these: 3659401 (21.88%) aligned 0 times 9911070 (59.25%) aligned exactly 1 time 3157400 (18.88%) aligned >1 times 78.12% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 1444719 / 13068470 = 0.1105 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 07:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.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 07:37:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:37:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:37:32: 1000000 INFO @ Tue, 14 Jul 2020 07:37:39: 2000000 INFO @ Tue, 14 Jul 2020 07:37:46: 3000000 INFO @ Tue, 14 Jul 2020 07:37:52: 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 07:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.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 07:37:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:37:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:37:59: 5000000 INFO @ Tue, 14 Jul 2020 07:38:02: 1000000 INFO @ Tue, 14 Jul 2020 07:38:06: 6000000 INFO @ Tue, 14 Jul 2020 07:38:09: 2000000 INFO @ Tue, 14 Jul 2020 07:38:13: 7000000 INFO @ Tue, 14 Jul 2020 07:38:16: 3000000 INFO @ Tue, 14 Jul 2020 07:38:21: 8000000 INFO @ Tue, 14 Jul 2020 07:38:23: 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 @ Tue, 14 Jul 2020 07:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.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 07:38:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:38:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:38:28: 9000000 INFO @ Tue, 14 Jul 2020 07:38:29: 5000000 INFO @ Tue, 14 Jul 2020 07:38:33: 1000000 INFO @ Tue, 14 Jul 2020 07:38:35: 10000000 INFO @ Tue, 14 Jul 2020 07:38:36: 6000000 INFO @ Tue, 14 Jul 2020 07:38:40: 2000000 INFO @ Tue, 14 Jul 2020 07:38:43: 11000000 INFO @ Tue, 14 Jul 2020 07:38:43: 7000000 INFO @ Tue, 14 Jul 2020 07:38:47: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:38:47: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:38:47: #1 total tags in treatment: 11623751 INFO @ Tue, 14 Jul 2020 07:38:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:38:47: #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 07:38:47: #1 tags after filtering in treatment: 11623751 INFO @ Tue, 14 Jul 2020 07:38:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:38:47: #1 finished! INFO @ Tue, 14 Jul 2020 07:38:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:38:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:38:48: 3000000 INFO @ Tue, 14 Jul 2020 07:38:48: #2 number of paired peaks: 478 WARNING @ Tue, 14 Jul 2020 07:38:48: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 14 Jul 2020 07:38:48: start model_add_line... INFO @ Tue, 14 Jul 2020 07:38:48: start X-correlation... INFO @ Tue, 14 Jul 2020 07:38:48: end of X-cor INFO @ Tue, 14 Jul 2020 07:38:48: #2 finished! INFO @ Tue, 14 Jul 2020 07:38:48: #2 predicted fragment length is 216 bps INFO @ Tue, 14 Jul 2020 07:38:48: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 14 Jul 2020 07:38:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.05_model.r INFO @ Tue, 14 Jul 2020 07:38:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:38:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:38:50: 8000000 INFO @ Tue, 14 Jul 2020 07:38:55: 4000000 INFO @ Tue, 14 Jul 2020 07:38:56: 9000000 INFO @ Tue, 14 Jul 2020 07:39:02: 5000000 INFO @ Tue, 14 Jul 2020 07:39:03: 10000000 INFO @ Tue, 14 Jul 2020 07:39:09: 6000000 INFO @ Tue, 14 Jul 2020 07:39:10: 11000000 INFO @ Tue, 14 Jul 2020 07:39:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:39:14: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:39:14: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:39:14: #1 total tags in treatment: 11623751 INFO @ Tue, 14 Jul 2020 07:39:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:39:14: #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 07:39:14: #1 tags after filtering in treatment: 11623751 INFO @ Tue, 14 Jul 2020 07:39:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:39:14: #1 finished! INFO @ Tue, 14 Jul 2020 07:39:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:39:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:39:15: #2 number of paired peaks: 478 WARNING @ Tue, 14 Jul 2020 07:39:15: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 14 Jul 2020 07:39:15: start model_add_line... INFO @ Tue, 14 Jul 2020 07:39:15: start X-correlation... INFO @ Tue, 14 Jul 2020 07:39:15: end of X-cor INFO @ Tue, 14 Jul 2020 07:39:15: #2 finished! INFO @ Tue, 14 Jul 2020 07:39:15: #2 predicted fragment length is 216 bps INFO @ Tue, 14 Jul 2020 07:39:15: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 14 Jul 2020 07:39:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.10_model.r INFO @ Tue, 14 Jul 2020 07:39:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:39:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:39:16: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:39:23: 8000000 INFO @ Tue, 14 Jul 2020 07:39:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:39:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:39:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.05_summits.bed INFO @ Tue, 14 Jul 2020 07:39:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2551 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:39:30: 9000000 INFO @ Tue, 14 Jul 2020 07:39:37: 10000000 INFO @ Tue, 14 Jul 2020 07:39:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:39:43: 11000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:39:48: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:39:48: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:39:48: #1 total tags in treatment: 11623751 INFO @ Tue, 14 Jul 2020 07:39:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:39:48: #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 07:39:48: #1 tags after filtering in treatment: 11623751 INFO @ Tue, 14 Jul 2020 07:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:39:48: #1 finished! INFO @ Tue, 14 Jul 2020 07:39:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:39:48: #2 number of paired peaks: 478 WARNING @ Tue, 14 Jul 2020 07:39:48: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 14 Jul 2020 07:39:48: start model_add_line... INFO @ Tue, 14 Jul 2020 07:39:49: start X-correlation... INFO @ Tue, 14 Jul 2020 07:39:49: end of X-cor INFO @ Tue, 14 Jul 2020 07:39:49: #2 finished! INFO @ Tue, 14 Jul 2020 07:39:49: #2 predicted fragment length is 216 bps INFO @ Tue, 14 Jul 2020 07:39:49: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 14 Jul 2020 07:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.20_model.r INFO @ Tue, 14 Jul 2020 07:39:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:39:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:39:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:39:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.10_summits.bed INFO @ Tue, 14 Jul 2020 07:39:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1665 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:40:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:40:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:40:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:40:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813084/SRX6813084.20_summits.bed INFO @ Tue, 14 Jul 2020 07:40:24: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1160 records, 4 fields): 23 millis CompletedMACS2peakCalling