Job ID = 6452395 SRX = SRX013032 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:44:36 prefetch.2.10.7: 1) Downloading 'SRR030298'... 2020-06-21T07:44:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:45:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:45:09 prefetch.2.10.7: 'SRR030298' is valid 2020-06-21T07:45:09 prefetch.2.10.7: 1) 'SRR030298' was downloaded successfully Read 2578040 spots for SRR030298/SRR030298.sra Written 2578040 spots for SRR030298/SRR030298.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: 00:00:01 Multiseed full-index search: 00:00:20 2578040 reads; of these: 2578040 (100.00%) were unpaired; of these: 1004724 (38.97%) aligned 0 times 1371574 (53.20%) aligned exactly 1 time 201742 (7.83%) aligned >1 times 61.03% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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] 90169 / 1573316 = 0.0573 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 16:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.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 16:46:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:46:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:46:34: 1000000 INFO @ Sun, 21 Jun 2020 16:46:37: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:46:37: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:46:37: #1 total tags in treatment: 1483147 INFO @ Sun, 21 Jun 2020 16:46:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:46:37: #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 16:46:37: #1 tags after filtering in treatment: 1482594 INFO @ Sun, 21 Jun 2020 16:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:46:37: #1 finished! INFO @ Sun, 21 Jun 2020 16:46:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:46:37: #2 number of paired peaks: 424 WARNING @ Sun, 21 Jun 2020 16:46:37: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sun, 21 Jun 2020 16:46:37: start model_add_line... INFO @ Sun, 21 Jun 2020 16:46:37: start X-correlation... INFO @ Sun, 21 Jun 2020 16:46:37: end of X-cor INFO @ Sun, 21 Jun 2020 16:46:37: #2 finished! INFO @ Sun, 21 Jun 2020 16:46:37: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 16:46:37: #2 alternative fragment length(s) may be 122,586 bps INFO @ Sun, 21 Jun 2020 16:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.05_model.r INFO @ Sun, 21 Jun 2020 16:46:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:46:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.05_summits.bed INFO @ Sun, 21 Jun 2020 16:46:43: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 16:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.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 16:46:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:46:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:47:03: 1000000 INFO @ Sun, 21 Jun 2020 16:47:06: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:47:06: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:47:06: #1 total tags in treatment: 1483147 INFO @ Sun, 21 Jun 2020 16:47:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:47:06: #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 16:47:06: #1 tags after filtering in treatment: 1482594 INFO @ Sun, 21 Jun 2020 16:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:47:06: #1 finished! INFO @ Sun, 21 Jun 2020 16:47:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:47:07: #2 number of paired peaks: 424 WARNING @ Sun, 21 Jun 2020 16:47:07: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sun, 21 Jun 2020 16:47:07: start model_add_line... INFO @ Sun, 21 Jun 2020 16:47:07: start X-correlation... INFO @ Sun, 21 Jun 2020 16:47:07: end of X-cor INFO @ Sun, 21 Jun 2020 16:47:07: #2 finished! INFO @ Sun, 21 Jun 2020 16:47:07: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 16:47:07: #2 alternative fragment length(s) may be 122,586 bps INFO @ Sun, 21 Jun 2020 16:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.10_model.r INFO @ Sun, 21 Jun 2020 16:47:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:47:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:47:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:47:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:47:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.10_summits.bed INFO @ Sun, 21 Jun 2020 16:47:12: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 16:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.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 16:47:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:47:29: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:47:34: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:47:37: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:47:37: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:47:37: #1 total tags in treatment: 1483147 INFO @ Sun, 21 Jun 2020 16:47:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:47:37: #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 16:47:37: #1 tags after filtering in treatment: 1482594 INFO @ Sun, 21 Jun 2020 16:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:47:37: #1 finished! INFO @ Sun, 21 Jun 2020 16:47:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:47:37: #2 number of paired peaks: 424 WARNING @ Sun, 21 Jun 2020 16:47:37: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sun, 21 Jun 2020 16:47:37: start model_add_line... INFO @ Sun, 21 Jun 2020 16:47:37: start X-correlation... INFO @ Sun, 21 Jun 2020 16:47:37: end of X-cor INFO @ Sun, 21 Jun 2020 16:47:37: #2 finished! INFO @ Sun, 21 Jun 2020 16:47:37: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 16:47:37: #2 alternative fragment length(s) may be 122,586 bps INFO @ Sun, 21 Jun 2020 16:47:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.20_model.r INFO @ Sun, 21 Jun 2020 16:47:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:47:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:47:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:47:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:47:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:47:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013032/SRX013032.20_summits.bed INFO @ Sun, 21 Jun 2020 16:47:43: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 1 millis CompletedMACS2peakCalling