Job ID = 6458428 SRX = SRX5226987 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:29:52 prefetch.2.10.7: 1) Downloading 'SRR8417902'... 2020-06-21T12:29:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:31:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:31:17 prefetch.2.10.7: 'SRR8417902' is valid 2020-06-21T12:31:17 prefetch.2.10.7: 1) 'SRR8417902' was downloaded successfully 2020-06-21T12:31:17 prefetch.2.10.7: 'SRR8417902' has 0 unresolved dependencies Read 4389430 spots for SRR8417902/SRR8417902.sra Written 4389430 spots for SRR8417902/SRR8417902.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: 00:02:42 4389430 reads; of these: 4389430 (100.00%) were unpaired; of these: 953851 (21.73%) aligned 0 times 938725 (21.39%) aligned exactly 1 time 2496854 (56.88%) aligned >1 times 78.27% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 1381686 / 3435579 = 0.4022 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 21:35:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.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 21:35:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:51: 1000000 INFO @ Sun, 21 Jun 2020 21:35:57: 2000000 INFO @ Sun, 21 Jun 2020 21:35:58: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:35:58: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:35:58: #1 total tags in treatment: 2053893 INFO @ Sun, 21 Jun 2020 21:35:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:58: #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 21:35:58: #1 tags after filtering in treatment: 2053648 INFO @ Sun, 21 Jun 2020 21:35:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:58: #2 number of paired peaks: 4248 INFO @ Sun, 21 Jun 2020 21:35:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:58: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 21:35:58: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 21 Jun 2020 21:35:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.05_model.r WARNING @ Sun, 21 Jun 2020 21:35:58: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:58: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Sun, 21 Jun 2020 21:35:58: #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 21:35:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.05_summits.bed INFO @ Sun, 21 Jun 2020 21:36:06: Done! pass1 - making usageList (740 chroms): 2 millis pass2 - checking and writing primary data (3092 records, 4 fields): 22 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 21:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.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 21:36:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:20: 1000000 INFO @ Sun, 21 Jun 2020 21:36:27: 2000000 INFO @ Sun, 21 Jun 2020 21:36:27: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:36:27: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:36:27: #1 total tags in treatment: 2053893 INFO @ Sun, 21 Jun 2020 21:36:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:27: #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 21:36:28: #1 tags after filtering in treatment: 2053648 INFO @ Sun, 21 Jun 2020 21:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:28: #2 number of paired peaks: 4248 INFO @ Sun, 21 Jun 2020 21:36:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:28: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 21:36:28: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 21 Jun 2020 21:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.10_model.r WARNING @ Sun, 21 Jun 2020 21:36:28: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:28: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Sun, 21 Jun 2020 21:36:28: #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 21:36:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.10_summits.bed INFO @ Sun, 21 Jun 2020 21:36:36: Done! pass1 - making usageList (594 chroms): 1 millis pass2 - checking and writing primary data (1919 records, 4 fields): 32 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 21:36:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.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 21:36:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:50: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:36:57: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:36:57: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:36:57: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:36:57: #1 total tags in treatment: 2053893 INFO @ Sun, 21 Jun 2020 21:36:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:57: #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 21:36:57: #1 tags after filtering in treatment: 2053648 INFO @ Sun, 21 Jun 2020 21:36:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:58: #2 number of paired peaks: 4248 INFO @ Sun, 21 Jun 2020 21:36:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:58: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 21:36:58: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 21 Jun 2020 21:36:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.20_model.r WARNING @ Sun, 21 Jun 2020 21:36:58: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:58: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Sun, 21 Jun 2020 21:36:58: #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 21:36:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:37:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226987/SRX5226987.20_summits.bed INFO @ Sun, 21 Jun 2020 21:37:05: Done! pass1 - making usageList (415 chroms): 1 millis pass2 - checking and writing primary data (855 records, 4 fields): 12 millis CompletedMACS2peakCalling