Job ID = 6626534 SRX = SRX6813073 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9352438 spots for SRR10080069/SRR10080069.sra Written 9352438 spots for SRR10080069/SRR10080069.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626650 ("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: 00:02:33 9352438 reads; of these: 9352438 (100.00%) were unpaired; of these: 3631311 (38.83%) aligned 0 times 4028128 (43.07%) aligned exactly 1 time 1692999 (18.10%) aligned >1 times 61.17% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 1103557 / 5721127 = 0.1929 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 07:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.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 07:25:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:25:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:25:52: 1000000 INFO @ Tue, 14 Jul 2020 07:25:58: 2000000 INFO @ Tue, 14 Jul 2020 07:26:04: 3000000 INFO @ Tue, 14 Jul 2020 07:26:10: 4000000 INFO @ Tue, 14 Jul 2020 07:26:14: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:26:14: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:26:14: #1 total tags in treatment: 4617570 INFO @ Tue, 14 Jul 2020 07:26:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:26:14: #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 07:26:14: #1 tags after filtering in treatment: 4617570 INFO @ Tue, 14 Jul 2020 07:26:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:26:14: #1 finished! INFO @ Tue, 14 Jul 2020 07:26:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:26:14: #2 number of paired peaks: 898 WARNING @ Tue, 14 Jul 2020 07:26:14: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Tue, 14 Jul 2020 07:26:14: start model_add_line... INFO @ Tue, 14 Jul 2020 07:26:14: start X-correlation... INFO @ Tue, 14 Jul 2020 07:26:14: end of X-cor INFO @ Tue, 14 Jul 2020 07:26:14: #2 finished! INFO @ Tue, 14 Jul 2020 07:26:14: #2 predicted fragment length is 154 bps INFO @ Tue, 14 Jul 2020 07:26:14: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 14 Jul 2020 07:26:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.05_model.r INFO @ Tue, 14 Jul 2020 07:26:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:26:14: #3 Pre-compute pvalue-qvalue table... 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 07:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.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 07:26:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:26:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:26:23: 1000000 INFO @ Tue, 14 Jul 2020 07:26:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:26:29: 2000000 INFO @ Tue, 14 Jul 2020 07:26:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:26:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:26:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.05_summits.bed INFO @ Tue, 14 Jul 2020 07:26:30: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2178 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:26:35: 3000000 INFO @ Tue, 14 Jul 2020 07:26:41: 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 07:26:45: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:26:45: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:26:45: #1 total tags in treatment: 4617570 INFO @ Tue, 14 Jul 2020 07:26:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:26:45: #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 07:26:45: #1 tags after filtering in treatment: 4617570 INFO @ Tue, 14 Jul 2020 07:26:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:26:45: #1 finished! INFO @ Tue, 14 Jul 2020 07:26:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:26:46: #2 number of paired peaks: 898 WARNING @ Tue, 14 Jul 2020 07:26:46: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Tue, 14 Jul 2020 07:26:46: start model_add_line... INFO @ Tue, 14 Jul 2020 07:26:46: start X-correlation... INFO @ Tue, 14 Jul 2020 07:26:46: end of X-cor INFO @ Tue, 14 Jul 2020 07:26:46: #2 finished! INFO @ Tue, 14 Jul 2020 07:26:46: #2 predicted fragment length is 154 bps INFO @ Tue, 14 Jul 2020 07:26:46: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 14 Jul 2020 07:26:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.10_model.r INFO @ Tue, 14 Jul 2020 07:26:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:26:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.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 07:26:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:26:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:26:53: 1000000 INFO @ Tue, 14 Jul 2020 07:26:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:26:58: 2000000 INFO @ Tue, 14 Jul 2020 07:27:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:27:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:27:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.10_summits.bed INFO @ Tue, 14 Jul 2020 07:27:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1573 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:27:04: 3000000 INFO @ Tue, 14 Jul 2020 07:27:11: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:27:14: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:27:14: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:27:14: #1 total tags in treatment: 4617570 INFO @ Tue, 14 Jul 2020 07:27:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:27:14: #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 07:27:14: #1 tags after filtering in treatment: 4617570 INFO @ Tue, 14 Jul 2020 07:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:27:14: #1 finished! INFO @ Tue, 14 Jul 2020 07:27:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:27:15: #2 number of paired peaks: 898 WARNING @ Tue, 14 Jul 2020 07:27:15: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Tue, 14 Jul 2020 07:27:15: start model_add_line... INFO @ Tue, 14 Jul 2020 07:27:15: start X-correlation... INFO @ Tue, 14 Jul 2020 07:27:15: end of X-cor INFO @ Tue, 14 Jul 2020 07:27:15: #2 finished! INFO @ Tue, 14 Jul 2020 07:27:15: #2 predicted fragment length is 154 bps INFO @ Tue, 14 Jul 2020 07:27:15: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 14 Jul 2020 07:27:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.20_model.r INFO @ Tue, 14 Jul 2020 07:27:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:27:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:27:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:27:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:27:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813073/SRX6813073.20_summits.bed INFO @ Tue, 14 Jul 2020 07:27:30: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1086 records, 4 fields): 14 millis CompletedMACS2peakCalling