Job ID = 6498615 SRX = SRX645124 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:44:38 prefetch.2.10.7: 1) Downloading 'SRR1505724'... 2020-06-25T23:44:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:48:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:48:53 prefetch.2.10.7: 1) 'SRR1505724' was downloaded successfully Read 27125148 spots for SRR1505724/SRR1505724.sra Written 27125148 spots for SRR1505724/SRR1505724.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: 00:09:24 27125148 reads; of these: 27125148 (100.00%) were unpaired; of these: 19392288 (71.49%) aligned 0 times 5621153 (20.72%) aligned exactly 1 time 2111707 (7.79%) aligned >1 times 28.51% overall alignment rate Time searching: 00:09:24 Overall time: 00:09:24 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] 3889435 / 7732860 = 0.5030 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 09:03:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.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 09:03:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:03:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:03:30: 1000000 INFO @ Fri, 26 Jun 2020 09:03:39: 2000000 INFO @ Fri, 26 Jun 2020 09:03:48: 3000000 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 09:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.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 09:03:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:03:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:03:55: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:03:55: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:03:55: #1 total tags in treatment: 3843425 INFO @ Fri, 26 Jun 2020 09:03:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:03:55: #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 09:03:55: #1 tags after filtering in treatment: 3843425 INFO @ Fri, 26 Jun 2020 09:03:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:03:55: #1 finished! INFO @ Fri, 26 Jun 2020 09:03:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:03:56: #2 number of paired peaks: 322 WARNING @ Fri, 26 Jun 2020 09:03:56: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Fri, 26 Jun 2020 09:03:56: start model_add_line... INFO @ Fri, 26 Jun 2020 09:03:56: start X-correlation... INFO @ Fri, 26 Jun 2020 09:03:56: end of X-cor INFO @ Fri, 26 Jun 2020 09:03:56: #2 finished! INFO @ Fri, 26 Jun 2020 09:03:56: #2 predicted fragment length is 82 bps INFO @ Fri, 26 Jun 2020 09:03:56: #2 alternative fragment length(s) may be 82 bps INFO @ Fri, 26 Jun 2020 09:03:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.05_model.r WARNING @ Fri, 26 Jun 2020 09:03:56: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:03:56: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Fri, 26 Jun 2020 09:03:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:03:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:03:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:04:00: 1000000 INFO @ Fri, 26 Jun 2020 09:04:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:04:09: 2000000 INFO @ Fri, 26 Jun 2020 09:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.05_summits.bed INFO @ Fri, 26 Jun 2020 09:04:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1515 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:04:18: 3000000 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 09:04:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.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 09:04:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:04:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:04:25: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:04:25: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:04:25: #1 total tags in treatment: 3843425 INFO @ Fri, 26 Jun 2020 09:04:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:04:25: #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 09:04:25: #1 tags after filtering in treatment: 3843425 INFO @ Fri, 26 Jun 2020 09:04:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:04:25: #1 finished! INFO @ Fri, 26 Jun 2020 09:04:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:04:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:04:26: #2 number of paired peaks: 322 WARNING @ Fri, 26 Jun 2020 09:04:26: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Fri, 26 Jun 2020 09:04:26: start model_add_line... INFO @ Fri, 26 Jun 2020 09:04:26: start X-correlation... INFO @ Fri, 26 Jun 2020 09:04:26: end of X-cor INFO @ Fri, 26 Jun 2020 09:04:26: #2 finished! INFO @ Fri, 26 Jun 2020 09:04:26: #2 predicted fragment length is 82 bps INFO @ Fri, 26 Jun 2020 09:04:26: #2 alternative fragment length(s) may be 82 bps INFO @ Fri, 26 Jun 2020 09:04:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.10_model.r WARNING @ Fri, 26 Jun 2020 09:04:26: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:04:26: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Fri, 26 Jun 2020 09:04:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:04:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:04:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:04:30: 1000000 INFO @ Fri, 26 Jun 2020 09:04:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:04:39: 2000000 INFO @ Fri, 26 Jun 2020 09:04:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:04:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:04:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.10_summits.bed INFO @ Fri, 26 Jun 2020 09:04:39: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (895 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:04:48: 3000000 INFO @ Fri, 26 Jun 2020 09:04:55: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:04:55: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:04:55: #1 total tags in treatment: 3843425 INFO @ Fri, 26 Jun 2020 09:04:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:04:55: #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 09:04:55: #1 tags after filtering in treatment: 3843425 INFO @ Fri, 26 Jun 2020 09:04:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:04:55: #1 finished! INFO @ Fri, 26 Jun 2020 09:04:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:04:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:04:56: #2 number of paired peaks: 322 WARNING @ Fri, 26 Jun 2020 09:04:56: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Fri, 26 Jun 2020 09:04:56: start model_add_line... INFO @ Fri, 26 Jun 2020 09:04:56: start X-correlation... INFO @ Fri, 26 Jun 2020 09:04:56: end of X-cor INFO @ Fri, 26 Jun 2020 09:04:56: #2 finished! INFO @ Fri, 26 Jun 2020 09:04:56: #2 predicted fragment length is 82 bps INFO @ Fri, 26 Jun 2020 09:04:56: #2 alternative fragment length(s) may be 82 bps INFO @ Fri, 26 Jun 2020 09:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.20_model.r WARNING @ Fri, 26 Jun 2020 09:04:56: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:04:56: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Fri, 26 Jun 2020 09:04:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:04:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:04:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:05:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:05:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645124/SRX645124.20_summits.bed INFO @ Fri, 26 Jun 2020 09:05:10: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (566 records, 4 fields): 2 millis CompletedMACS2peakCalling