Job ID = 6455689 SRX = SRX287990 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:13:06 prefetch.2.10.7: 1) Downloading 'SRR870179'... 2020-06-21T10:13:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:15:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:15:10 prefetch.2.10.7: 'SRR870179' is valid 2020-06-21T10:15:10 prefetch.2.10.7: 1) 'SRR870179' was downloaded successfully Read 14962039 spots for SRR870179/SRR870179.sra Written 14962039 spots for SRR870179/SRR870179.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: 00:03:06 14962039 reads; of these: 14962039 (100.00%) were unpaired; of these: 1173623 (7.84%) aligned 0 times 12650552 (84.55%) aligned exactly 1 time 1137864 (7.61%) aligned >1 times 92.16% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 1328408 / 13788416 = 0.0963 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 19:22:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.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 19:22:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:00: 1000000 INFO @ Sun, 21 Jun 2020 19:23:05: 2000000 INFO @ Sun, 21 Jun 2020 19:23:10: 3000000 INFO @ Sun, 21 Jun 2020 19:23:15: 4000000 INFO @ Sun, 21 Jun 2020 19:23:19: 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 19:23:24: 6000000 INFO @ Sun, 21 Jun 2020 19:23:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.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 19:23:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:29: 7000000 INFO @ Sun, 21 Jun 2020 19:23:31: 1000000 INFO @ Sun, 21 Jun 2020 19:23:35: 8000000 INFO @ Sun, 21 Jun 2020 19:23:36: 2000000 INFO @ Sun, 21 Jun 2020 19:23:40: 9000000 INFO @ Sun, 21 Jun 2020 19:23:42: 3000000 INFO @ Sun, 21 Jun 2020 19:23:45: 10000000 INFO @ Sun, 21 Jun 2020 19:23:48: 4000000 INFO @ Sun, 21 Jun 2020 19:23:50: 11000000 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 19:23:53: 5000000 INFO @ Sun, 21 Jun 2020 19:23:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.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 19:23:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:56: 12000000 INFO @ Sun, 21 Jun 2020 19:23:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:58: #1 total tags in treatment: 12460008 INFO @ Sun, 21 Jun 2020 19:23:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:58: #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 19:23:59: #1 tags after filtering in treatment: 12459982 INFO @ Sun, 21 Jun 2020 19:23:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:59: 6000000 INFO @ Sun, 21 Jun 2020 19:24:00: #2 number of paired peaks: 507 WARNING @ Sun, 21 Jun 2020 19:24:00: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:00: #2 predicted fragment length is 158 bps INFO @ Sun, 21 Jun 2020 19:24:00: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 21 Jun 2020 19:24:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.05_model.r INFO @ Sun, 21 Jun 2020 19:24:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:00: 1000000 INFO @ Sun, 21 Jun 2020 19:24:05: 7000000 INFO @ Sun, 21 Jun 2020 19:24:05: 2000000 INFO @ Sun, 21 Jun 2020 19:24:10: 3000000 INFO @ Sun, 21 Jun 2020 19:24:11: 8000000 INFO @ Sun, 21 Jun 2020 19:24:15: 4000000 INFO @ Sun, 21 Jun 2020 19:24:16: 9000000 INFO @ Sun, 21 Jun 2020 19:24:20: 5000000 INFO @ Sun, 21 Jun 2020 19:24:22: 10000000 INFO @ Sun, 21 Jun 2020 19:24:26: 6000000 INFO @ Sun, 21 Jun 2020 19:24:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:28: 11000000 INFO @ Sun, 21 Jun 2020 19:24:31: 7000000 INFO @ Sun, 21 Jun 2020 19:24:34: 12000000 INFO @ Sun, 21 Jun 2020 19:24:36: 8000000 INFO @ Sun, 21 Jun 2020 19:24:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:37: #1 total tags in treatment: 12460008 INFO @ Sun, 21 Jun 2020 19:24:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:37: #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 19:24:38: #1 tags after filtering in treatment: 12459982 INFO @ Sun, 21 Jun 2020 19:24:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:38: #2 number of paired peaks: 507 WARNING @ Sun, 21 Jun 2020 19:24:38: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:39: #2 predicted fragment length is 158 bps INFO @ Sun, 21 Jun 2020 19:24:39: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 21 Jun 2020 19:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.10_model.r INFO @ Sun, 21 Jun 2020 19:24:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:41: 9000000 INFO @ Sun, 21 Jun 2020 19:24:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.05_summits.bed INFO @ Sun, 21 Jun 2020 19:24:42: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (4202 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:46: 10000000 INFO @ Sun, 21 Jun 2020 19:24:51: 11000000 INFO @ Sun, 21 Jun 2020 19:24:56: 12000000 INFO @ Sun, 21 Jun 2020 19:24:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:58: #1 total tags in treatment: 12460008 INFO @ Sun, 21 Jun 2020 19:24:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:58: #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 19:24:59: #1 tags after filtering in treatment: 12459982 INFO @ Sun, 21 Jun 2020 19:24:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:59: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:25:00: #2 number of paired peaks: 507 WARNING @ Sun, 21 Jun 2020 19:25:00: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:00: #2 predicted fragment length is 158 bps INFO @ Sun, 21 Jun 2020 19:25:00: #2 alternative fragment length(s) may be 158 bps INFO @ Sun, 21 Jun 2020 19:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.20_model.r INFO @ Sun, 21 Jun 2020 19:25:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.10_summits.bed INFO @ Sun, 21 Jun 2020 19:25:21: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (1917 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:25:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287990/SRX287990.20_summits.bed INFO @ Sun, 21 Jun 2020 19:25:39: Done! pass1 - making usageList (42 chroms): 0 millis pass2 - checking and writing primary data (440 records, 4 fields): 3 millis CompletedMACS2peakCalling