Job ID = 16439189 SRX = SRX15206466 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:44:16 prefetch.2.10.7: 1) Downloading 'SRR19139340'... 2022-08-02T05:44:16 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:44:25 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:44:25 prefetch.2.10.7: 'SRR19139340' is valid 2022-08-02T05:44:25 prefetch.2.10.7: 1) 'SRR19139340' was downloaded successfully 2022-08-02T05:44:25 prefetch.2.10.7: 'SRR19139340' has 0 unresolved dependencies Read 3971877 spots for SRR19139340/SRR19139340.sra Written 3971877 spots for SRR19139340/SRR19139340.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439284 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:57 3971877 reads; of these: 3971877 (100.00%) were unpaired; of these: 121507 (3.06%) aligned 0 times 1331300 (33.52%) aligned exactly 1 time 2519070 (63.42%) aligned >1 times 96.94% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 1054736 / 3850370 = 0.2739 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.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, 02 Aug 2022 14:49:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:32: 1000000 INFO @ Tue, 02 Aug 2022 14:49:39: 2000000 INFO @ Tue, 02 Aug 2022 14:49:44: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:49:44: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:49:44: #1 total tags in treatment: 2795634 INFO @ Tue, 02 Aug 2022 14:49:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:49:44: #1 tags after filtering in treatment: 2795634 INFO @ Tue, 02 Aug 2022 14:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:44: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:49:45: #2 number of paired peaks: 6937 INFO @ Tue, 02 Aug 2022 14:49:45: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:45: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:45: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:45: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:45: #2 predicted fragment length is 288 bps INFO @ Tue, 02 Aug 2022 14:49:45: #2 alternative fragment length(s) may be 288 bps INFO @ Tue, 02 Aug 2022 14:49:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.05_model.r INFO @ Tue, 02 Aug 2022 14:49:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:45: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:49:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.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, 02 Aug 2022 14:49:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:01: 1000000 INFO @ Tue, 02 Aug 2022 14:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.05_summits.bed INFO @ Tue, 02 Aug 2022 14:50:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8361 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:08: 2000000 INFO @ Tue, 02 Aug 2022 14:50:14: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:50:14: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:50:14: #1 total tags in treatment: 2795634 INFO @ Tue, 02 Aug 2022 14:50:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:50:14: #1 tags after filtering in treatment: 2795634 INFO @ Tue, 02 Aug 2022 14:50:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:14: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:15: #2 number of paired peaks: 6937 INFO @ Tue, 02 Aug 2022 14:50:15: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:15: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:15: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:15: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:15: #2 predicted fragment length is 288 bps INFO @ Tue, 02 Aug 2022 14:50:15: #2 alternative fragment length(s) may be 288 bps INFO @ Tue, 02 Aug 2022 14:50:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.10_model.r INFO @ Tue, 02 Aug 2022 14:50:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.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, 02 Aug 2022 14:50:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:30: 1000000 INFO @ Tue, 02 Aug 2022 14:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.10_summits.bed INFO @ Tue, 02 Aug 2022 14:50:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6588 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:37: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:50:42: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:50:42: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:50:42: #1 total tags in treatment: 2795634 INFO @ Tue, 02 Aug 2022 14:50:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:50:42: #1 tags after filtering in treatment: 2795634 INFO @ Tue, 02 Aug 2022 14:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:42: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:43: #2 number of paired peaks: 6937 INFO @ Tue, 02 Aug 2022 14:50:43: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:43: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:43: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:43: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:43: #2 predicted fragment length is 288 bps INFO @ Tue, 02 Aug 2022 14:50:43: #2 alternative fragment length(s) may be 288 bps INFO @ Tue, 02 Aug 2022 14:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.20_model.r INFO @ Tue, 02 Aug 2022 14:50:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:50:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206466/SRX15206466.20_summits.bed INFO @ Tue, 02 Aug 2022 14:51:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4520 records, 4 fields): 20 millis CompletedMACS2peakCalling