Job ID = 6508760 SRX = SRX467116 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:45:54 prefetch.2.10.7: 1) Downloading 'SRR1164540'... 2020-06-26T14:45:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:47:16 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:47:17 prefetch.2.10.7: 'SRR1164540' is valid 2020-06-26T14:47:17 prefetch.2.10.7: 1) 'SRR1164540' was downloaded successfully Read 13175493 spots for SRR1164540/SRR1164540.sra Written 13175493 spots for SRR1164540/SRR1164540.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: 00:04:41 13175493 reads; of these: 13175493 (100.00%) were unpaired; of these: 877928 (6.66%) aligned 0 times 7753121 (58.85%) aligned exactly 1 time 4544444 (34.49%) aligned >1 times 93.34% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1679913 / 12297565 = 0.1366 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 23:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.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 23:57:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:57:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:57:24: 1000000 INFO @ Fri, 26 Jun 2020 23:57:30: 2000000 INFO @ Fri, 26 Jun 2020 23:57:36: 3000000 INFO @ Fri, 26 Jun 2020 23:57:43: 4000000 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 23:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.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 23:57:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:57:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:57:49: 5000000 INFO @ Fri, 26 Jun 2020 23:57:54: 1000000 INFO @ Fri, 26 Jun 2020 23:57:55: 6000000 INFO @ Fri, 26 Jun 2020 23:58:01: 2000000 INFO @ Fri, 26 Jun 2020 23:58:02: 7000000 INFO @ Fri, 26 Jun 2020 23:58:08: 3000000 INFO @ Fri, 26 Jun 2020 23:58:08: 8000000 INFO @ Fri, 26 Jun 2020 23:58:14: 4000000 INFO @ Fri, 26 Jun 2020 23:58:15: 9000000 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 23:58:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.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 23:58:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:58:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:58:21: 5000000 INFO @ Fri, 26 Jun 2020 23:58:22: 10000000 INFO @ Fri, 26 Jun 2020 23:58:25: 1000000 INFO @ Fri, 26 Jun 2020 23:58:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:58:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:58:27: #1 total tags in treatment: 10617652 INFO @ Fri, 26 Jun 2020 23:58:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:58:27: #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 23:58:27: 6000000 INFO @ Fri, 26 Jun 2020 23:58:27: #1 tags after filtering in treatment: 10617544 INFO @ Fri, 26 Jun 2020 23:58:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:58:27: #1 finished! INFO @ Fri, 26 Jun 2020 23:58:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:58:28: #2 number of paired peaks: 2208 INFO @ Fri, 26 Jun 2020 23:58:28: start model_add_line... INFO @ Fri, 26 Jun 2020 23:58:28: start X-correlation... INFO @ Fri, 26 Jun 2020 23:58:28: end of X-cor INFO @ Fri, 26 Jun 2020 23:58:28: #2 finished! INFO @ Fri, 26 Jun 2020 23:58:28: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 23:58:28: #2 alternative fragment length(s) may be 2,49,582 bps INFO @ Fri, 26 Jun 2020 23:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.05_model.r WARNING @ Fri, 26 Jun 2020 23:58:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:58:29: #2 You may need to consider one of the other alternative d(s): 2,49,582 WARNING @ Fri, 26 Jun 2020 23:58:29: #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 23:58:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:58:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:58:31: 2000000 INFO @ Fri, 26 Jun 2020 23:58:34: 7000000 INFO @ Fri, 26 Jun 2020 23:58:38: 3000000 INFO @ Fri, 26 Jun 2020 23:58:40: 8000000 INFO @ Fri, 26 Jun 2020 23:58:45: 4000000 INFO @ Fri, 26 Jun 2020 23:58:47: 9000000 INFO @ Fri, 26 Jun 2020 23:58:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:58:51: 5000000 INFO @ Fri, 26 Jun 2020 23:58:54: 10000000 INFO @ Fri, 26 Jun 2020 23:58:58: 6000000 INFO @ Fri, 26 Jun 2020 23:58:58: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:58:58: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:58:58: #1 total tags in treatment: 10617652 INFO @ Fri, 26 Jun 2020 23:58:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:58:58: #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 23:58:59: #1 tags after filtering in treatment: 10617544 INFO @ Fri, 26 Jun 2020 23:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:58:59: #1 finished! INFO @ Fri, 26 Jun 2020 23:58:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:59:00: #2 number of paired peaks: 2208 INFO @ Fri, 26 Jun 2020 23:59:00: start model_add_line... INFO @ Fri, 26 Jun 2020 23:59:00: start X-correlation... INFO @ Fri, 26 Jun 2020 23:59:00: end of X-cor INFO @ Fri, 26 Jun 2020 23:59:00: #2 finished! INFO @ Fri, 26 Jun 2020 23:59:00: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 23:59:00: #2 alternative fragment length(s) may be 2,49,582 bps INFO @ Fri, 26 Jun 2020 23:59:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.10_model.r WARNING @ Fri, 26 Jun 2020 23:59:00: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:59:00: #2 You may need to consider one of the other alternative d(s): 2,49,582 WARNING @ Fri, 26 Jun 2020 23:59:00: #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 23:59:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:59:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.05_summits.bed INFO @ Fri, 26 Jun 2020 23:59:00: Done! pass1 - making usageList (647 chroms): 1 millis pass2 - checking and writing primary data (2787 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:59:04: 7000000 INFO @ Fri, 26 Jun 2020 23:59:10: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:59:18: 9000000 INFO @ Fri, 26 Jun 2020 23:59:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:59:24: 10000000 INFO @ Fri, 26 Jun 2020 23:59:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:59:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:59:28: #1 total tags in treatment: 10617652 INFO @ Fri, 26 Jun 2020 23:59:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:59:28: #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 23:59:29: #1 tags after filtering in treatment: 10617544 INFO @ Fri, 26 Jun 2020 23:59:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:59:29: #1 finished! INFO @ Fri, 26 Jun 2020 23:59:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:59:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:59:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:59:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:59:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.10_summits.bed INFO @ Fri, 26 Jun 2020 23:59:30: Done! INFO @ Fri, 26 Jun 2020 23:59:30: #2 number of paired peaks: 2208 INFO @ Fri, 26 Jun 2020 23:59:30: start model_add_line... pass1 - making usageList (526 chroms): 1 millis pass2 - checking and writing primary data (2075 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:59:30: start X-correlation... INFO @ Fri, 26 Jun 2020 23:59:30: end of X-cor INFO @ Fri, 26 Jun 2020 23:59:30: #2 finished! INFO @ Fri, 26 Jun 2020 23:59:30: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 23:59:30: #2 alternative fragment length(s) may be 2,49,582 bps INFO @ Fri, 26 Jun 2020 23:59:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.20_model.r WARNING @ Fri, 26 Jun 2020 23:59:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:59:30: #2 You may need to consider one of the other alternative d(s): 2,49,582 WARNING @ Fri, 26 Jun 2020 23:59:30: #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 23:59:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:59:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:59:50: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:00:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:00:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:00:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467116/SRX467116.20_summits.bed INFO @ Sat, 27 Jun 2020 00:00:01: Done! pass1 - making usageList (360 chroms): 1 millis pass2 - checking and writing primary data (842 records, 4 fields): 21 millis CompletedMACS2peakCalling