Job ID = 6453825 SRX = SRX151956 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:38:47 prefetch.2.10.7: 1) Downloading 'SRR504790'... 2020-06-21T08:38:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:39:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:39:36 prefetch.2.10.7: 'SRR504790' is valid 2020-06-21T08:39:36 prefetch.2.10.7: 1) 'SRR504790' was downloaded successfully Read 7687834 spots for SRR504790/SRR504790.sra Written 7687834 spots for SRR504790/SRR504790.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: 00:01:26 7687834 reads; of these: 7687834 (100.00%) were unpaired; of these: 480835 (6.25%) aligned 0 times 5394756 (70.17%) aligned exactly 1 time 1812243 (23.57%) aligned >1 times 93.75% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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] 731857 / 7206999 = 0.1015 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 17:43:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.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 17:43:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:43:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:26: 1000000 INFO @ Sun, 21 Jun 2020 17:43:31: 2000000 INFO @ Sun, 21 Jun 2020 17:43:35: 3000000 INFO @ Sun, 21 Jun 2020 17:43:40: 4000000 INFO @ Sun, 21 Jun 2020 17:43:45: 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 17:43:50: 6000000 INFO @ Sun, 21 Jun 2020 17:43:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.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 17:43:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:43:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:43:53: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:43:53: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:43:53: #1 total tags in treatment: 6475142 INFO @ Sun, 21 Jun 2020 17:43:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:43:53: #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 17:43:53: #1 tags after filtering in treatment: 6475128 INFO @ Sun, 21 Jun 2020 17:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:43:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:43:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:43:54: #2 number of paired peaks: 958 WARNING @ Sun, 21 Jun 2020 17:43:54: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sun, 21 Jun 2020 17:43:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:43:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:43:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:43:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:43:54: #2 predicted fragment length is 109 bps INFO @ Sun, 21 Jun 2020 17:43:54: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 21 Jun 2020 17:43:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.05_model.r INFO @ Sun, 21 Jun 2020 17:43:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:43:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:43:57: 1000000 INFO @ Sun, 21 Jun 2020 17:44:02: 2000000 INFO @ Sun, 21 Jun 2020 17:44:08: 3000000 INFO @ Sun, 21 Jun 2020 17:44:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:44:13: 4000000 INFO @ Sun, 21 Jun 2020 17:44:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:44:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:44:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.05_summits.bed INFO @ Sun, 21 Jun 2020 17:44:17: Done! pass1 - making usageList (451 chroms): 2 millis pass2 - checking and writing primary data (4625 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:44:19: 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 17:44:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.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 17:44:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:25: 6000000 INFO @ Sun, 21 Jun 2020 17:44:26: 1000000 INFO @ Sun, 21 Jun 2020 17:44:28: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:44:28: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:44:28: #1 total tags in treatment: 6475142 INFO @ Sun, 21 Jun 2020 17:44:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:44:28: #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 17:44:28: #1 tags after filtering in treatment: 6475128 INFO @ Sun, 21 Jun 2020 17:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:44:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:44:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:44:29: #2 number of paired peaks: 958 WARNING @ Sun, 21 Jun 2020 17:44:29: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sun, 21 Jun 2020 17:44:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:44:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:44:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:44:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:44:29: #2 predicted fragment length is 109 bps INFO @ Sun, 21 Jun 2020 17:44:29: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 21 Jun 2020 17:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.10_model.r INFO @ Sun, 21 Jun 2020 17:44:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:44:32: 2000000 INFO @ Sun, 21 Jun 2020 17:44:36: 3000000 INFO @ Sun, 21 Jun 2020 17:44:41: 4000000 INFO @ Sun, 21 Jun 2020 17:44:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:44:46: 5000000 INFO @ Sun, 21 Jun 2020 17:44:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:44:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:44:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.10_summits.bed INFO @ Sun, 21 Jun 2020 17:44:51: Done! INFO @ Sun, 21 Jun 2020 17:44:51: 6000000 pass1 - making usageList (229 chroms): 1 millis pass2 - checking and writing primary data (1943 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:44:54: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:44:54: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:44:54: #1 total tags in treatment: 6475142 INFO @ Sun, 21 Jun 2020 17:44:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:44:54: #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 17:44:54: #1 tags after filtering in treatment: 6475128 INFO @ Sun, 21 Jun 2020 17:44:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:44:54: #1 finished! INFO @ Sun, 21 Jun 2020 17:44:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:44:54: #2 number of paired peaks: 958 WARNING @ Sun, 21 Jun 2020 17:44:54: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sun, 21 Jun 2020 17:44:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:44:55: start X-correlation... INFO @ Sun, 21 Jun 2020 17:44:55: end of X-cor INFO @ Sun, 21 Jun 2020 17:44:55: #2 finished! INFO @ Sun, 21 Jun 2020 17:44:55: #2 predicted fragment length is 109 bps INFO @ Sun, 21 Jun 2020 17:44:55: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 21 Jun 2020 17:44:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.20_model.r INFO @ Sun, 21 Jun 2020 17:44:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:44:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:45:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX151956/SRX151956.20_summits.bed INFO @ Sun, 21 Jun 2020 17:45:17: Done! pass1 - making usageList (134 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 7 millis CompletedMACS2peakCalling