Job ID = 6459859 SRX = SRX914955 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:40:47 prefetch.2.10.7: 1) Downloading 'SRR1873265'... 2020-06-21T13:40:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:44:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:44:45 prefetch.2.10.7: 1) 'SRR1873265' was downloaded successfully Read 28633023 spots for SRR1873265/SRR1873265.sra Written 28633023 spots for SRR1873265/SRR1873265.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: 00:04:36 28633023 reads; of these: 28633023 (100.00%) were unpaired; of these: 2047996 (7.15%) aligned 0 times 24193330 (84.49%) aligned exactly 1 time 2391697 (8.35%) aligned >1 times 92.85% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5783817 / 26585027 = 0.2176 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 @ Sun, 21 Jun 2020 22:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.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 @ Sun, 21 Jun 2020 22:56:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:56:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:56:56: 1000000 INFO @ Sun, 21 Jun 2020 22:57:01: 2000000 INFO @ Sun, 21 Jun 2020 22:57:06: 3000000 INFO @ Sun, 21 Jun 2020 22:57:11: 4000000 INFO @ Sun, 21 Jun 2020 22:57:16: 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 @ Sun, 21 Jun 2020 22:57:21: 6000000 INFO @ Sun, 21 Jun 2020 22:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.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 @ Sun, 21 Jun 2020 22:57:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:57:26: 7000000 INFO @ Sun, 21 Jun 2020 22:57:27: 1000000 INFO @ Sun, 21 Jun 2020 22:57:31: 8000000 INFO @ Sun, 21 Jun 2020 22:57:32: 2000000 INFO @ Sun, 21 Jun 2020 22:57:36: 9000000 INFO @ Sun, 21 Jun 2020 22:57:37: 3000000 INFO @ Sun, 21 Jun 2020 22:57:41: 10000000 INFO @ Sun, 21 Jun 2020 22:57:42: 4000000 INFO @ Sun, 21 Jun 2020 22:57:45: 11000000 INFO @ Sun, 21 Jun 2020 22:57:47: 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 @ Sun, 21 Jun 2020 22:57:51: 12000000 INFO @ Sun, 21 Jun 2020 22:57:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.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 @ Sun, 21 Jun 2020 22:57:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:57:52: 6000000 INFO @ Sun, 21 Jun 2020 22:57:56: 13000000 INFO @ Sun, 21 Jun 2020 22:57:57: 1000000 INFO @ Sun, 21 Jun 2020 22:57:58: 7000000 INFO @ Sun, 21 Jun 2020 22:58:01: 14000000 INFO @ Sun, 21 Jun 2020 22:58:02: 2000000 INFO @ Sun, 21 Jun 2020 22:58:03: 8000000 INFO @ Sun, 21 Jun 2020 22:58:06: 15000000 INFO @ Sun, 21 Jun 2020 22:58:07: 3000000 INFO @ Sun, 21 Jun 2020 22:58:08: 9000000 INFO @ Sun, 21 Jun 2020 22:58:11: 16000000 INFO @ Sun, 21 Jun 2020 22:58:12: 4000000 INFO @ Sun, 21 Jun 2020 22:58:13: 10000000 INFO @ Sun, 21 Jun 2020 22:58:16: 17000000 INFO @ Sun, 21 Jun 2020 22:58:17: 5000000 INFO @ Sun, 21 Jun 2020 22:58:19: 11000000 INFO @ Sun, 21 Jun 2020 22:58:21: 18000000 INFO @ Sun, 21 Jun 2020 22:58:23: 6000000 INFO @ Sun, 21 Jun 2020 22:58:24: 12000000 INFO @ Sun, 21 Jun 2020 22:58:27: 19000000 INFO @ Sun, 21 Jun 2020 22:58:28: 7000000 INFO @ Sun, 21 Jun 2020 22:58:29: 13000000 INFO @ Sun, 21 Jun 2020 22:58:32: 20000000 INFO @ Sun, 21 Jun 2020 22:58:33: 8000000 INFO @ Sun, 21 Jun 2020 22:58:34: 14000000 INFO @ Sun, 21 Jun 2020 22:58:36: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:58:36: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:58:36: #1 total tags in treatment: 20801210 INFO @ Sun, 21 Jun 2020 22:58:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:58:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:58:37: #1 tags after filtering in treatment: 20801079 INFO @ Sun, 21 Jun 2020 22:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:58:37: #1 finished! INFO @ Sun, 21 Jun 2020 22:58:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:58:38: 9000000 INFO @ Sun, 21 Jun 2020 22:58:38: #2 number of paired peaks: 363 WARNING @ Sun, 21 Jun 2020 22:58:38: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 21 Jun 2020 22:58:38: start model_add_line... INFO @ Sun, 21 Jun 2020 22:58:39: start X-correlation... INFO @ Sun, 21 Jun 2020 22:58:39: end of X-cor INFO @ Sun, 21 Jun 2020 22:58:39: #2 finished! INFO @ Sun, 21 Jun 2020 22:58:39: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 22:58:39: #2 alternative fragment length(s) may be 4,150 bps INFO @ Sun, 21 Jun 2020 22:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.05_model.r INFO @ Sun, 21 Jun 2020 22:58:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:58:40: 15000000 INFO @ Sun, 21 Jun 2020 22:58:44: 10000000 INFO @ Sun, 21 Jun 2020 22:58:45: 16000000 INFO @ Sun, 21 Jun 2020 22:58:49: 11000000 INFO @ Sun, 21 Jun 2020 22:58:51: 17000000 INFO @ Sun, 21 Jun 2020 22:58:54: 12000000 INFO @ Sun, 21 Jun 2020 22:58:56: 18000000 INFO @ Sun, 21 Jun 2020 22:58:59: 13000000 INFO @ Sun, 21 Jun 2020 22:59:01: 19000000 INFO @ Sun, 21 Jun 2020 22:59:04: 14000000 INFO @ Sun, 21 Jun 2020 22:59:06: 20000000 INFO @ Sun, 21 Jun 2020 22:59:09: 15000000 INFO @ Sun, 21 Jun 2020 22:59:11: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:59:11: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:59:11: #1 total tags in treatment: 20801210 INFO @ Sun, 21 Jun 2020 22:59:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:59:11: #1 tags after filtering in treatment: 20801079 INFO @ Sun, 21 Jun 2020 22:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:13: #2 number of paired peaks: 363 WARNING @ Sun, 21 Jun 2020 22:59:13: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 21 Jun 2020 22:59:13: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:13: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:13: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:13: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:13: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 22:59:13: #2 alternative fragment length(s) may be 4,150 bps INFO @ Sun, 21 Jun 2020 22:59:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.10_model.r INFO @ Sun, 21 Jun 2020 22:59:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:15: 16000000 INFO @ Sun, 21 Jun 2020 22:59:20: 17000000 INFO @ Sun, 21 Jun 2020 22:59:25: 18000000 INFO @ Sun, 21 Jun 2020 22:59:26: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:59:30: 19000000 INFO @ Sun, 21 Jun 2020 22:59:35: 20000000 INFO @ Sun, 21 Jun 2020 22:59:40: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:59:40: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:59:40: #1 total tags in treatment: 20801210 INFO @ Sun, 21 Jun 2020 22:59:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:59:40: #1 tags after filtering in treatment: 20801079 INFO @ Sun, 21 Jun 2020 22:59:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:40: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:42: #2 number of paired peaks: 363 WARNING @ Sun, 21 Jun 2020 22:59:42: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 21 Jun 2020 22:59:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:42: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 22:59:42: #2 alternative fragment length(s) may be 4,150 bps INFO @ Sun, 21 Jun 2020 22:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.20_model.r INFO @ Sun, 21 Jun 2020 22:59:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:59:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:59:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.05_summits.bed INFO @ Sun, 21 Jun 2020 22:59:50: Done! pass1 - making usageList (99 chroms): 2 millis pass2 - checking and writing primary data (9232 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:00:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:00:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:00:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:00:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.10_summits.bed INFO @ Sun, 21 Jun 2020 23:00:23: Done! pass1 - making usageList (88 chroms): 2 millis pass2 - checking and writing primary data (5560 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:00:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914955/SRX914955.20_summits.bed INFO @ Sun, 21 Jun 2020 23:00:52: Done! pass1 - making usageList (72 chroms): 1 millis pass2 - checking and writing primary data (1696 records, 4 fields): 5 millis CompletedMACS2peakCalling