Job ID = 6458419 SRX = SRX5226978 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:27:37 prefetch.2.10.7: 1) Downloading 'SRR8417893'... 2020-06-21T12:27:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:29:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:29:23 prefetch.2.10.7: 'SRR8417893' is valid 2020-06-21T12:29:23 prefetch.2.10.7: 1) 'SRR8417893' was downloaded successfully 2020-06-21T12:29:23 prefetch.2.10.7: 'SRR8417893' has 0 unresolved dependencies Read 5711649 spots for SRR8417893/SRR8417893.sra Written 5711649 spots for SRR8417893/SRR8417893.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: 00:03:36 5711649 reads; of these: 5711649 (100.00%) were unpaired; of these: 1351787 (23.67%) aligned 0 times 1314666 (23.02%) aligned exactly 1 time 3045196 (53.32%) aligned >1 times 76.33% overall alignment rate Time searching: 00:03:36 Overall time: 00:03:36 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] 1631454 / 4359862 = 0.3742 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 21:35:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.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 21:35:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:19: 1000000 INFO @ Sun, 21 Jun 2020 21:35:25: 2000000 INFO @ Sun, 21 Jun 2020 21:35:30: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:35:30: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:35:30: #1 total tags in treatment: 2728408 INFO @ Sun, 21 Jun 2020 21:35:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:30: #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 21:35:30: #1 tags after filtering in treatment: 2728173 INFO @ Sun, 21 Jun 2020 21:35:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:31: #2 number of paired peaks: 4547 INFO @ Sun, 21 Jun 2020 21:35:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:31: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 21:35:31: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 21:35:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.05_model.r WARNING @ Sun, 21 Jun 2020 21:35:31: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:31: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sun, 21 Jun 2020 21:35:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:35:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:39: #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 @ Sun, 21 Jun 2020 21:35:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.05_summits.bed INFO @ Sun, 21 Jun 2020 21:35:42: Done! INFO @ Sun, 21 Jun 2020 21:35:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.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 21:35:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:43: #1 read treatment tags... pass1 - making usageList (767 chroms): 2 millis pass2 - checking and writing primary data (3696 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:35:49: 1000000 INFO @ Sun, 21 Jun 2020 21:35:55: 2000000 INFO @ Sun, 21 Jun 2020 21:36:00: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:36:00: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:36:00: #1 total tags in treatment: 2728408 INFO @ Sun, 21 Jun 2020 21:36:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:00: #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 21:36:00: #1 tags after filtering in treatment: 2728173 INFO @ Sun, 21 Jun 2020 21:36:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:01: #2 number of paired peaks: 4547 INFO @ Sun, 21 Jun 2020 21:36:01: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:01: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:01: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:01: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:01: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 21:36:01: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 21:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.10_model.r WARNING @ Sun, 21 Jun 2020 21:36:01: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:01: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sun, 21 Jun 2020 21:36:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:36:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:08: #3 Call peaks for each chromosome... 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 21:36:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.10_summits.bed INFO @ Sun, 21 Jun 2020 21:36:11: Done! pass1 - making usageList (654 chroms): 2 millis pass2 - checking and writing primary data (2349 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.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 21:36:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:19: 1000000 INFO @ Sun, 21 Jun 2020 21:36:25: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:36:30: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:36:30: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:36:30: #1 total tags in treatment: 2728408 INFO @ Sun, 21 Jun 2020 21:36:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:30: #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 21:36:30: #1 tags after filtering in treatment: 2728173 INFO @ Sun, 21 Jun 2020 21:36:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:30: #2 number of paired peaks: 4547 INFO @ Sun, 21 Jun 2020 21:36:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:30: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 21:36:30: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 21:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.20_model.r WARNING @ Sun, 21 Jun 2020 21:36:30: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:30: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sun, 21 Jun 2020 21:36:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:36:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:36:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226978/SRX5226978.20_summits.bed INFO @ Sun, 21 Jun 2020 21:36:41: Done! pass1 - making usageList (493 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 15 millis CompletedMACS2peakCalling