Job ID = 6509164 SRX = SRX699541 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:16:58 prefetch.2.10.7: 1) Downloading 'SRR1573540'... 2020-06-26T15:16:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:18:26 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:18:27 prefetch.2.10.7: 'SRR1573540' is valid 2020-06-26T15:18:27 prefetch.2.10.7: 1) 'SRR1573540' was downloaded successfully Read 17762885 spots for SRR1573540/SRR1573540.sra Written 17762885 spots for SRR1573540/SRR1573540.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:42 17762885 reads; of these: 17762885 (100.00%) were unpaired; of these: 3568851 (20.09%) aligned 0 times 12740944 (71.73%) aligned exactly 1 time 1453090 (8.18%) aligned >1 times 79.91% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 4410876 / 14194034 = 0.3108 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 @ Sat, 27 Jun 2020 00:25:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.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 @ Sat, 27 Jun 2020 00:25:48: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:25:48: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:25:53: 1000000 INFO @ Sat, 27 Jun 2020 00:25:58: 2000000 INFO @ Sat, 27 Jun 2020 00:26:03: 3000000 INFO @ Sat, 27 Jun 2020 00:26:08: 4000000 INFO @ Sat, 27 Jun 2020 00:26:13: 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 @ Sat, 27 Jun 2020 00:26:18: 6000000 INFO @ Sat, 27 Jun 2020 00:26:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.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 @ Sat, 27 Jun 2020 00:26:19: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:26:19: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:26:24: 7000000 INFO @ Sat, 27 Jun 2020 00:26:24: 1000000 INFO @ Sat, 27 Jun 2020 00:26:29: 8000000 INFO @ Sat, 27 Jun 2020 00:26:29: 2000000 INFO @ Sat, 27 Jun 2020 00:26:34: 9000000 INFO @ Sat, 27 Jun 2020 00:26:35: 3000000 INFO @ Sat, 27 Jun 2020 00:26:39: #1 tag size is determined as 36 bps INFO @ Sat, 27 Jun 2020 00:26:39: #1 tag size = 36 INFO @ Sat, 27 Jun 2020 00:26:39: #1 total tags in treatment: 9783158 INFO @ Sat, 27 Jun 2020 00:26:39: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:26:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:26:39: #1 tags after filtering in treatment: 9782855 INFO @ Sat, 27 Jun 2020 00:26:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:26:39: #1 finished! INFO @ Sat, 27 Jun 2020 00:26:39: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:26:40: 4000000 INFO @ Sat, 27 Jun 2020 00:26:40: #2 number of paired peaks: 2306 INFO @ Sat, 27 Jun 2020 00:26:40: start model_add_line... INFO @ Sat, 27 Jun 2020 00:26:40: start X-correlation... INFO @ Sat, 27 Jun 2020 00:26:40: end of X-cor INFO @ Sat, 27 Jun 2020 00:26:40: #2 finished! INFO @ Sat, 27 Jun 2020 00:26:40: #2 predicted fragment length is 145 bps INFO @ Sat, 27 Jun 2020 00:26:40: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 27 Jun 2020 00:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.05_model.r INFO @ Sat, 27 Jun 2020 00:26:40: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:26:45: 5000000 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 @ Sat, 27 Jun 2020 00:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.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 @ Sat, 27 Jun 2020 00:26:48: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:26:48: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:26:51: 6000000 INFO @ Sat, 27 Jun 2020 00:26:54: 1000000 INFO @ Sat, 27 Jun 2020 00:26:56: 7000000 INFO @ Sat, 27 Jun 2020 00:26:59: 2000000 INFO @ Sat, 27 Jun 2020 00:27:02: 8000000 INFO @ Sat, 27 Jun 2020 00:27:04: 3000000 INFO @ Sat, 27 Jun 2020 00:27:07: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:27:07: 9000000 INFO @ Sat, 27 Jun 2020 00:27:09: 4000000 INFO @ Sat, 27 Jun 2020 00:27:12: #1 tag size is determined as 36 bps INFO @ Sat, 27 Jun 2020 00:27:12: #1 tag size = 36 INFO @ Sat, 27 Jun 2020 00:27:12: #1 total tags in treatment: 9783158 INFO @ Sat, 27 Jun 2020 00:27:12: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:27:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:27:12: #1 tags after filtering in treatment: 9782855 INFO @ Sat, 27 Jun 2020 00:27:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:27:12: #1 finished! INFO @ Sat, 27 Jun 2020 00:27:12: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:27:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:27:13: #2 number of paired peaks: 2306 INFO @ Sat, 27 Jun 2020 00:27:13: start model_add_line... INFO @ Sat, 27 Jun 2020 00:27:13: start X-correlation... INFO @ Sat, 27 Jun 2020 00:27:13: end of X-cor INFO @ Sat, 27 Jun 2020 00:27:13: #2 finished! INFO @ Sat, 27 Jun 2020 00:27:13: #2 predicted fragment length is 145 bps INFO @ Sat, 27 Jun 2020 00:27:13: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 27 Jun 2020 00:27:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.10_model.r INFO @ Sat, 27 Jun 2020 00:27:13: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:27:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:27:15: 5000000 INFO @ Sat, 27 Jun 2020 00:27:20: 6000000 INFO @ Sat, 27 Jun 2020 00:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:27:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.05_summits.bed INFO @ Sat, 27 Jun 2020 00:27:22: Done! pass1 - making usageList (96 chroms): 2 millis pass2 - checking and writing primary data (7358 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:27:25: 7000000 INFO @ Sat, 27 Jun 2020 00:27:31: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:27:36: 9000000 INFO @ Sat, 27 Jun 2020 00:27:40: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:27:40: #1 tag size is determined as 36 bps INFO @ Sat, 27 Jun 2020 00:27:40: #1 tag size = 36 INFO @ Sat, 27 Jun 2020 00:27:40: #1 total tags in treatment: 9783158 INFO @ Sat, 27 Jun 2020 00:27:40: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:27:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:27:41: #1 tags after filtering in treatment: 9782855 INFO @ Sat, 27 Jun 2020 00:27:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:27:41: #1 finished! INFO @ Sat, 27 Jun 2020 00:27:41: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:27:42: #2 number of paired peaks: 2306 INFO @ Sat, 27 Jun 2020 00:27:42: start model_add_line... INFO @ Sat, 27 Jun 2020 00:27:42: start X-correlation... INFO @ Sat, 27 Jun 2020 00:27:42: end of X-cor INFO @ Sat, 27 Jun 2020 00:27:42: #2 finished! INFO @ Sat, 27 Jun 2020 00:27:42: #2 predicted fragment length is 145 bps INFO @ Sat, 27 Jun 2020 00:27:42: #2 alternative fragment length(s) may be 145 bps INFO @ Sat, 27 Jun 2020 00:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.20_model.r INFO @ Sat, 27 Jun 2020 00:27:42: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:27:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:27:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:27:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.10_summits.bed INFO @ Sat, 27 Jun 2020 00:27:54: Done! pass1 - making usageList (90 chroms): 2 millis pass2 - checking and writing primary data (5596 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:28:07: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:28:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:28:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:28:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX699541/SRX699541.20_summits.bed INFO @ Sat, 27 Jun 2020 00:28:21: Done! pass1 - making usageList (79 chroms): 2 millis pass2 - checking and writing primary data (3850 records, 4 fields): 8 millis CompletedMACS2peakCalling