Job ID = 6459458 SRX = SRX681798 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:04:01 prefetch.2.10.7: 1) Downloading 'SRR1552267'... 2020-06-21T13:04:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:05:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:05:28 prefetch.2.10.7: 'SRR1552267' is valid 2020-06-21T13:05:28 prefetch.2.10.7: 1) 'SRR1552267' was downloaded successfully Read 4437102 spots for SRR1552267/SRR1552267.sra Written 4437102 spots for SRR1552267/SRR1552267.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: 00:00:46 4437102 reads; of these: 4437102 (100.00%) were unpaired; of these: 461310 (10.40%) aligned 0 times 3473654 (78.29%) aligned exactly 1 time 502138 (11.32%) aligned >1 times 89.60% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 1639959 / 3975792 = 0.4125 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 22:07:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.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 22:07:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:52: 1000000 INFO @ Sun, 21 Jun 2020 22:07:58: 2000000 INFO @ Sun, 21 Jun 2020 22:07:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 22:07:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 22:07:59: #1 total tags in treatment: 2335833 INFO @ Sun, 21 Jun 2020 22:07:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:59: #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 22:08:00: #1 tags after filtering in treatment: 2335628 INFO @ Sun, 21 Jun 2020 22:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:08:00: #1 finished! INFO @ Sun, 21 Jun 2020 22:08:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:08:00: #2 number of paired peaks: 313 WARNING @ Sun, 21 Jun 2020 22:08:00: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 21 Jun 2020 22:08:00: start model_add_line... INFO @ Sun, 21 Jun 2020 22:08:00: start X-correlation... INFO @ Sun, 21 Jun 2020 22:08:00: end of X-cor INFO @ Sun, 21 Jun 2020 22:08:00: #2 finished! INFO @ Sun, 21 Jun 2020 22:08:00: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:08:00: #2 alternative fragment length(s) may be 79 bps INFO @ Sun, 21 Jun 2020 22:08:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.05_model.r INFO @ Sun, 21 Jun 2020 22:08:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:08:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:08:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.05_summits.bed INFO @ Sun, 21 Jun 2020 22:08:09: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 3 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 22:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.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 22:08:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:21: 1000000 INFO @ Sun, 21 Jun 2020 22:08:27: 2000000 INFO @ Sun, 21 Jun 2020 22:08:29: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 22:08:29: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 22:08:29: #1 total tags in treatment: 2335833 INFO @ Sun, 21 Jun 2020 22:08:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:08:29: #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 22:08:29: #1 tags after filtering in treatment: 2335628 INFO @ Sun, 21 Jun 2020 22:08:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:08:29: #1 finished! INFO @ Sun, 21 Jun 2020 22:08:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:08:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:08:29: #2 number of paired peaks: 313 WARNING @ Sun, 21 Jun 2020 22:08:29: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 21 Jun 2020 22:08:29: start model_add_line... INFO @ Sun, 21 Jun 2020 22:08:29: start X-correlation... INFO @ Sun, 21 Jun 2020 22:08:29: end of X-cor INFO @ Sun, 21 Jun 2020 22:08:29: #2 finished! INFO @ Sun, 21 Jun 2020 22:08:29: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:08:29: #2 alternative fragment length(s) may be 79 bps INFO @ Sun, 21 Jun 2020 22:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.10_model.r INFO @ Sun, 21 Jun 2020 22:08:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:08:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.10_summits.bed INFO @ Sun, 21 Jun 2020 22:08:38: Done! pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 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 22:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.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 22:08:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:51: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:08:57: 2000000 INFO @ Sun, 21 Jun 2020 22:08:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 22:08:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 22:08:59: #1 total tags in treatment: 2335833 INFO @ Sun, 21 Jun 2020 22:08:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:08:59: #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 22:08:59: #1 tags after filtering in treatment: 2335628 INFO @ Sun, 21 Jun 2020 22:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:08:59: #1 finished! INFO @ Sun, 21 Jun 2020 22:08:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:08:59: #2 number of paired peaks: 313 WARNING @ Sun, 21 Jun 2020 22:08:59: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 21 Jun 2020 22:08:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:08:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:08:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:08:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:08:59: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:08:59: #2 alternative fragment length(s) may be 79 bps INFO @ Sun, 21 Jun 2020 22:08:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.20_model.r INFO @ Sun, 21 Jun 2020 22:08:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:08:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:09:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX681798/SRX681798.20_summits.bed INFO @ Sun, 21 Jun 2020 22:09:08: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 1 millis CompletedMACS2peakCalling