Job ID = 6626532 SRX = SRX6813071 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14070723 spots for SRR10080071/SRR10080071.sra Written 14070723 spots for SRR10080071/SRR10080071.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626653 ("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: 00:03:01 14070723 reads; of these: 14070723 (100.00%) were unpaired; of these: 2539362 (18.05%) aligned 0 times 10481366 (74.49%) aligned exactly 1 time 1049995 (7.46%) aligned >1 times 81.95% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 4249821 / 11531361 = 0.3685 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 07:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.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 07:27:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:27:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:27:23: 1000000 INFO @ Tue, 14 Jul 2020 07:27:28: 2000000 INFO @ Tue, 14 Jul 2020 07:27:34: 3000000 INFO @ Tue, 14 Jul 2020 07:27:39: 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 07:27:45: 5000000 INFO @ Tue, 14 Jul 2020 07:27:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.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 07:27:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:27:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:27:51: 6000000 INFO @ Tue, 14 Jul 2020 07:27:53: 1000000 INFO @ Tue, 14 Jul 2020 07:27:57: 7000000 INFO @ Tue, 14 Jul 2020 07:27:59: 2000000 INFO @ Tue, 14 Jul 2020 07:27:59: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:27:59: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:27:59: #1 total tags in treatment: 7281540 INFO @ Tue, 14 Jul 2020 07:27:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:27:59: #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 07:27:59: #1 tags after filtering in treatment: 7281540 INFO @ Tue, 14 Jul 2020 07:27:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:27:59: #1 finished! INFO @ Tue, 14 Jul 2020 07:27:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:28:00: #2 number of paired peaks: 6626 INFO @ Tue, 14 Jul 2020 07:28:00: start model_add_line... INFO @ Tue, 14 Jul 2020 07:28:00: start X-correlation... INFO @ Tue, 14 Jul 2020 07:28:00: end of X-cor INFO @ Tue, 14 Jul 2020 07:28:00: #2 finished! INFO @ Tue, 14 Jul 2020 07:28:00: #2 predicted fragment length is 231 bps INFO @ Tue, 14 Jul 2020 07:28:00: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 14 Jul 2020 07:28:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.05_model.r INFO @ Tue, 14 Jul 2020 07:28:00: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:28:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:28:05: 3000000 INFO @ Tue, 14 Jul 2020 07:28:10: 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 07:28:16: 5000000 INFO @ Tue, 14 Jul 2020 07:28:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.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 07:28:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:28:22: 6000000 INFO @ Tue, 14 Jul 2020 07:28:23: 1000000 INFO @ Tue, 14 Jul 2020 07:28:28: 7000000 INFO @ Tue, 14 Jul 2020 07:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:28:29: 2000000 INFO @ Tue, 14 Jul 2020 07:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.05_summits.bed INFO @ Tue, 14 Jul 2020 07:28:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9778 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:28:30: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:28:30: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:28:30: #1 total tags in treatment: 7281540 INFO @ Tue, 14 Jul 2020 07:28:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:28:30: #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 07:28:30: #1 tags after filtering in treatment: 7281540 INFO @ Tue, 14 Jul 2020 07:28:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:28:30: #1 finished! INFO @ Tue, 14 Jul 2020 07:28:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:28:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:28:31: #2 number of paired peaks: 6626 INFO @ Tue, 14 Jul 2020 07:28:31: start model_add_line... INFO @ Tue, 14 Jul 2020 07:28:31: start X-correlation... INFO @ Tue, 14 Jul 2020 07:28:31: end of X-cor INFO @ Tue, 14 Jul 2020 07:28:31: #2 finished! INFO @ Tue, 14 Jul 2020 07:28:31: #2 predicted fragment length is 231 bps INFO @ Tue, 14 Jul 2020 07:28:31: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 14 Jul 2020 07:28:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.10_model.r INFO @ Tue, 14 Jul 2020 07:28:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:28:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:28:35: 3000000 INFO @ Tue, 14 Jul 2020 07:28:41: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:28:47: 5000000 INFO @ Tue, 14 Jul 2020 07:28:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:28:52: 6000000 INFO @ Tue, 14 Jul 2020 07:28:58: 7000000 INFO @ Tue, 14 Jul 2020 07:28:59: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:28:59: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:28:59: #1 total tags in treatment: 7281540 INFO @ Tue, 14 Jul 2020 07:28:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:28:59: #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 07:28:59: #1 tags after filtering in treatment: 7281540 INFO @ Tue, 14 Jul 2020 07:28:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:28:59: #1 finished! INFO @ Tue, 14 Jul 2020 07:28:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:28:59: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:29:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:00: #2 number of paired peaks: 6626 INFO @ Tue, 14 Jul 2020 07:29:00: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:00: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:00: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:00: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:00: #2 predicted fragment length is 231 bps INFO @ Tue, 14 Jul 2020 07:29:00: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 14 Jul 2020 07:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.20_model.r INFO @ Tue, 14 Jul 2020 07:29:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.10_summits.bed INFO @ Tue, 14 Jul 2020 07:29:00: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:29:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7910 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:29:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:29:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813071/SRX6813071.20_summits.bed INFO @ Tue, 14 Jul 2020 07:29:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6200 records, 4 fields): 23 millis CompletedMACS2peakCalling