Job ID = 6626533 SRX = SRX6813072 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11071117 spots for SRR10080070/SRR10080070.sra Written 11071117 spots for SRR10080070/SRR10080070.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626649 ("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: 00:02:30 11071117 reads; of these: 11071117 (100.00%) were unpaired; of these: 3289688 (29.71%) aligned 0 times 6060684 (54.74%) aligned exactly 1 time 1720745 (15.54%) aligned >1 times 70.29% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 903522 / 7781429 = 0.1161 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 07:26:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.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 07:26:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:26:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:26:10: 1000000 INFO @ Tue, 14 Jul 2020 07:26:16: 2000000 INFO @ Tue, 14 Jul 2020 07:26:21: 3000000 INFO @ Tue, 14 Jul 2020 07:26:26: 4000000 INFO @ Tue, 14 Jul 2020 07:26:31: 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 07:26:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.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 07:26:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:26:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:26:37: 6000000 INFO @ Tue, 14 Jul 2020 07:26:42: 1000000 INFO @ Tue, 14 Jul 2020 07:26:42: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:26:42: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:26:42: #1 total tags in treatment: 6877907 INFO @ Tue, 14 Jul 2020 07:26:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:26:42: #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 07:26:43: #1 tags after filtering in treatment: 6877907 INFO @ Tue, 14 Jul 2020 07:26:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:26:43: #1 finished! INFO @ Tue, 14 Jul 2020 07:26:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:26:43: #2 number of paired peaks: 682 WARNING @ Tue, 14 Jul 2020 07:26:43: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Tue, 14 Jul 2020 07:26:43: start model_add_line... INFO @ Tue, 14 Jul 2020 07:26:43: start X-correlation... INFO @ Tue, 14 Jul 2020 07:26:43: end of X-cor INFO @ Tue, 14 Jul 2020 07:26:43: #2 finished! INFO @ Tue, 14 Jul 2020 07:26:43: #2 predicted fragment length is 212 bps INFO @ Tue, 14 Jul 2020 07:26:43: #2 alternative fragment length(s) may be 212 bps INFO @ Tue, 14 Jul 2020 07:26:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.05_model.r INFO @ Tue, 14 Jul 2020 07:26:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:26:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:26:49: 2000000 INFO @ Tue, 14 Jul 2020 07:26:56: 3000000 INFO @ Tue, 14 Jul 2020 07:26:58: #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 07:27:03: 4000000 INFO @ Tue, 14 Jul 2020 07:27:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.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 07:27:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:27:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:27:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.05_summits.bed INFO @ Tue, 14 Jul 2020 07:27:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3339 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:27:11: 5000000 INFO @ Tue, 14 Jul 2020 07:27:11: 1000000 INFO @ Tue, 14 Jul 2020 07:27:17: 2000000 INFO @ Tue, 14 Jul 2020 07:27:18: 6000000 INFO @ Tue, 14 Jul 2020 07:27:23: 3000000 INFO @ Tue, 14 Jul 2020 07:27:24: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:27:24: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:27:24: #1 total tags in treatment: 6877907 INFO @ Tue, 14 Jul 2020 07:27:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:27:24: #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 07:27:24: #1 tags after filtering in treatment: 6877907 INFO @ Tue, 14 Jul 2020 07:27:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:27:24: #1 finished! INFO @ Tue, 14 Jul 2020 07:27:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:27:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:27:25: #2 number of paired peaks: 682 WARNING @ Tue, 14 Jul 2020 07:27:25: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Tue, 14 Jul 2020 07:27:25: start model_add_line... INFO @ Tue, 14 Jul 2020 07:27:25: start X-correlation... INFO @ Tue, 14 Jul 2020 07:27:25: end of X-cor INFO @ Tue, 14 Jul 2020 07:27:25: #2 finished! INFO @ Tue, 14 Jul 2020 07:27:25: #2 predicted fragment length is 212 bps INFO @ Tue, 14 Jul 2020 07:27:25: #2 alternative fragment length(s) may be 212 bps INFO @ Tue, 14 Jul 2020 07:27:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.10_model.r INFO @ Tue, 14 Jul 2020 07:27:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:27:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:27:29: 4000000 INFO @ Tue, 14 Jul 2020 07:27:35: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:27:41: 6000000 INFO @ Tue, 14 Jul 2020 07:27:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:27:46: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:27:46: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:27:46: #1 total tags in treatment: 6877907 INFO @ Tue, 14 Jul 2020 07:27:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:27:46: #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 07:27:46: #1 tags after filtering in treatment: 6877907 INFO @ Tue, 14 Jul 2020 07:27:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:27:46: #1 finished! INFO @ Tue, 14 Jul 2020 07:27:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:27:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:27:46: #2 number of paired peaks: 682 WARNING @ Tue, 14 Jul 2020 07:27:46: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Tue, 14 Jul 2020 07:27:46: start model_add_line... INFO @ Tue, 14 Jul 2020 07:27:46: start X-correlation... INFO @ Tue, 14 Jul 2020 07:27:46: end of X-cor INFO @ Tue, 14 Jul 2020 07:27:46: #2 finished! INFO @ Tue, 14 Jul 2020 07:27:46: #2 predicted fragment length is 212 bps INFO @ Tue, 14 Jul 2020 07:27:46: #2 alternative fragment length(s) may be 212 bps INFO @ Tue, 14 Jul 2020 07:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.20_model.r INFO @ Tue, 14 Jul 2020 07:27:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:27:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:27:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:27:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.10_summits.bed INFO @ Tue, 14 Jul 2020 07:27:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1852 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:28:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:28:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:28:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:28:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813072/SRX6813072.20_summits.bed INFO @ Tue, 14 Jul 2020 07:28:09: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1137 records, 4 fields): 27 millis CompletedMACS2peakCalling