Job ID = 6498701 SRX = SRX706814 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:54:44 prefetch.2.10.7: 1) Downloading 'SRR1581495'... 2020-06-25T23:54:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:57:44 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:57:44 prefetch.2.10.7: 1) 'SRR1581495' was downloaded successfully Read 21233132 spots for SRR1581495/SRR1581495.sra Written 21233132 spots for SRR1581495/SRR1581495.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: 00:04:19 21233132 reads; of these: 21233132 (100.00%) were unpaired; of these: 8785661 (41.38%) aligned 0 times 9073811 (42.73%) aligned exactly 1 time 3373660 (15.89%) aligned >1 times 58.62% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 5474050 / 12447471 = 0.4398 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 @ Fri, 26 Jun 2020 09:05:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.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 @ Fri, 26 Jun 2020 09:05:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:05:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:06:04: 1000000 INFO @ Fri, 26 Jun 2020 09:06:09: 2000000 INFO @ Fri, 26 Jun 2020 09:06:14: 3000000 INFO @ Fri, 26 Jun 2020 09:06:19: 4000000 INFO @ Fri, 26 Jun 2020 09:06:24: 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 @ Fri, 26 Jun 2020 09:06:30: 6000000 INFO @ Fri, 26 Jun 2020 09:06:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.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 @ Fri, 26 Jun 2020 09:06:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:06:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:06:35: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:06:35: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:06:35: #1 total tags in treatment: 6973421 INFO @ Fri, 26 Jun 2020 09:06:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:06:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:06:35: #1 tags after filtering in treatment: 6973421 INFO @ Fri, 26 Jun 2020 09:06:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:06:35: #1 finished! INFO @ Fri, 26 Jun 2020 09:06:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:06:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:06:35: 1000000 INFO @ Fri, 26 Jun 2020 09:06:35: #2 number of paired peaks: 382 WARNING @ Fri, 26 Jun 2020 09:06:35: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Fri, 26 Jun 2020 09:06:35: start model_add_line... INFO @ Fri, 26 Jun 2020 09:06:35: start X-correlation... INFO @ Fri, 26 Jun 2020 09:06:35: end of X-cor INFO @ Fri, 26 Jun 2020 09:06:35: #2 finished! INFO @ Fri, 26 Jun 2020 09:06:35: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 09:06:35: #2 alternative fragment length(s) may be 2,145,168,564 bps INFO @ Fri, 26 Jun 2020 09:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.05_model.r INFO @ Fri, 26 Jun 2020 09:06:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:06:40: 2000000 INFO @ Fri, 26 Jun 2020 09:06:45: 3000000 INFO @ Fri, 26 Jun 2020 09:06:51: 4000000 INFO @ Fri, 26 Jun 2020 09:06:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:06:56: 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 @ Fri, 26 Jun 2020 09:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.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 @ Fri, 26 Jun 2020 09:06:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:06:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:07:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:07:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:07:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.05_summits.bed INFO @ Fri, 26 Jun 2020 09:07:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1323 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:07:01: 6000000 INFO @ Fri, 26 Jun 2020 09:07:05: 1000000 INFO @ Fri, 26 Jun 2020 09:07:06: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:07:06: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:07:06: #1 total tags in treatment: 6973421 INFO @ Fri, 26 Jun 2020 09:07:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:07:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:07:06: #1 tags after filtering in treatment: 6973421 INFO @ Fri, 26 Jun 2020 09:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:07:06: #1 finished! INFO @ Fri, 26 Jun 2020 09:07:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:07:07: #2 number of paired peaks: 382 WARNING @ Fri, 26 Jun 2020 09:07:07: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Fri, 26 Jun 2020 09:07:07: start model_add_line... INFO @ Fri, 26 Jun 2020 09:07:07: start X-correlation... INFO @ Fri, 26 Jun 2020 09:07:07: end of X-cor INFO @ Fri, 26 Jun 2020 09:07:07: #2 finished! INFO @ Fri, 26 Jun 2020 09:07:07: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 09:07:07: #2 alternative fragment length(s) may be 2,145,168,564 bps INFO @ Fri, 26 Jun 2020 09:07:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.10_model.r INFO @ Fri, 26 Jun 2020 09:07:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:07:10: 2000000 INFO @ Fri, 26 Jun 2020 09:07:15: 3000000 INFO @ Fri, 26 Jun 2020 09:07:20: 4000000 INFO @ Fri, 26 Jun 2020 09:07:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:07:25: 5000000 INFO @ Fri, 26 Jun 2020 09:07:30: 6000000 INFO @ Fri, 26 Jun 2020 09:07:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:07:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:07:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.10_summits.bed INFO @ Fri, 26 Jun 2020 09:07:31: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (420 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:07:35: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:07:35: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:07:35: #1 total tags in treatment: 6973421 INFO @ Fri, 26 Jun 2020 09:07:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:07:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:07:35: #1 tags after filtering in treatment: 6973421 INFO @ Fri, 26 Jun 2020 09:07:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:07:35: #1 finished! INFO @ Fri, 26 Jun 2020 09:07:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:07:36: #2 number of paired peaks: 382 WARNING @ Fri, 26 Jun 2020 09:07:36: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Fri, 26 Jun 2020 09:07:36: start model_add_line... INFO @ Fri, 26 Jun 2020 09:07:36: start X-correlation... INFO @ Fri, 26 Jun 2020 09:07:36: end of X-cor INFO @ Fri, 26 Jun 2020 09:07:36: #2 finished! INFO @ Fri, 26 Jun 2020 09:07:36: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 09:07:36: #2 alternative fragment length(s) may be 2,145,168,564 bps INFO @ Fri, 26 Jun 2020 09:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.20_model.r INFO @ Fri, 26 Jun 2020 09:07:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:07:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:07:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:08:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:08:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:08:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706814/SRX706814.20_summits.bed INFO @ Fri, 26 Jun 2020 09:08:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (106 records, 4 fields): 1 millis CompletedMACS2peakCalling