Job ID = 6498600 SRX = SRX645109 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:31:11 prefetch.2.10.7: 1) Downloading 'SRR1505708'... 2020-06-26T00:31:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:37:46 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:37:46 prefetch.2.10.7: 1) 'SRR1505708' was downloaded successfully Read 33543582 spots for SRR1505708/SRR1505708.sra Written 33543582 spots for SRR1505708/SRR1505708.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: 00:11:47 33543582 reads; of these: 33543582 (100.00%) were unpaired; of these: 25637562 (76.43%) aligned 0 times 6228877 (18.57%) aligned exactly 1 time 1677143 (5.00%) aligned >1 times 23.57% overall alignment rate Time searching: 00:11:47 Overall time: 00:11:47 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] 5465293 / 7906020 = 0.6913 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 09:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.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 09:55:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:55:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:55:14: 1000000 INFO @ Fri, 26 Jun 2020 09:55:22: 2000000 INFO @ Fri, 26 Jun 2020 09:55:25: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:55:25: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:55:25: #1 total tags in treatment: 2440727 INFO @ Fri, 26 Jun 2020 09:55:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:55:25: #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 09:55:25: #1 tags after filtering in treatment: 2440727 INFO @ Fri, 26 Jun 2020 09:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:55:25: #1 finished! INFO @ Fri, 26 Jun 2020 09:55:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:55:25: #2 number of paired peaks: 790 WARNING @ Fri, 26 Jun 2020 09:55:25: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Fri, 26 Jun 2020 09:55:25: start model_add_line... INFO @ Fri, 26 Jun 2020 09:55:25: start X-correlation... INFO @ Fri, 26 Jun 2020 09:55:25: end of X-cor INFO @ Fri, 26 Jun 2020 09:55:25: #2 finished! INFO @ Fri, 26 Jun 2020 09:55:25: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 09:55:25: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 26 Jun 2020 09:55:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.05_model.r WARNING @ Fri, 26 Jun 2020 09:55:25: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:55:25: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 26 Jun 2020 09:55:25: #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 09:55:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:55:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:55:32: #3 Call peaks for each chromosome... 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 09:55:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:55:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:55:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.05_summits.bed INFO @ Fri, 26 Jun 2020 09:55:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2061 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.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 09:55:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:55:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:55:44: 1000000 INFO @ Fri, 26 Jun 2020 09:55:51: 2000000 INFO @ Fri, 26 Jun 2020 09:55:54: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:55:54: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:55:54: #1 total tags in treatment: 2440727 INFO @ Fri, 26 Jun 2020 09:55:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:55:54: #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 09:55:55: #1 tags after filtering in treatment: 2440727 INFO @ Fri, 26 Jun 2020 09:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:55:55: #1 finished! INFO @ Fri, 26 Jun 2020 09:55:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:55:55: #2 number of paired peaks: 790 WARNING @ Fri, 26 Jun 2020 09:55:55: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Fri, 26 Jun 2020 09:55:55: start model_add_line... INFO @ Fri, 26 Jun 2020 09:55:55: start X-correlation... INFO @ Fri, 26 Jun 2020 09:55:55: end of X-cor INFO @ Fri, 26 Jun 2020 09:55:55: #2 finished! INFO @ Fri, 26 Jun 2020 09:55:55: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 09:55:55: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 26 Jun 2020 09:55:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.10_model.r WARNING @ Fri, 26 Jun 2020 09:55:55: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:55:55: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 26 Jun 2020 09:55:55: #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 09:55:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:56:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:56:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:56:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:56:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.10_summits.bed INFO @ Fri, 26 Jun 2020 09:56:04: Done! 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 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (894 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.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 09:56:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:56:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:56:15: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:56:24: 2000000 INFO @ Fri, 26 Jun 2020 09:56:27: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:56:27: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:56:27: #1 total tags in treatment: 2440727 INFO @ Fri, 26 Jun 2020 09:56:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:56:27: #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 09:56:27: #1 tags after filtering in treatment: 2440727 INFO @ Fri, 26 Jun 2020 09:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:56:27: #1 finished! INFO @ Fri, 26 Jun 2020 09:56:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:56:28: #2 number of paired peaks: 790 WARNING @ Fri, 26 Jun 2020 09:56:28: Fewer paired peaks (790) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 790 pairs to build model! INFO @ Fri, 26 Jun 2020 09:56:28: start model_add_line... INFO @ Fri, 26 Jun 2020 09:56:28: start X-correlation... INFO @ Fri, 26 Jun 2020 09:56:28: end of X-cor INFO @ Fri, 26 Jun 2020 09:56:28: #2 finished! INFO @ Fri, 26 Jun 2020 09:56:28: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 09:56:28: #2 alternative fragment length(s) may be 88 bps INFO @ Fri, 26 Jun 2020 09:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.20_model.r WARNING @ Fri, 26 Jun 2020 09:56:28: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:56:28: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Fri, 26 Jun 2020 09:56:28: #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 09:56:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:56:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:56:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:56:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:56:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:56:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645109/SRX645109.20_summits.bed INFO @ Fri, 26 Jun 2020 09:56:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (499 records, 4 fields): 2 millis CompletedMACS2peakCalling