Job ID = 6527473 SRX = SRX025466 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:50:12 prefetch.2.10.7: 1) Downloading 'SRR063860'... 2020-06-29T12:50:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:52:28 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:52:28 prefetch.2.10.7: 'SRR063860' is valid 2020-06-29T12:52:28 prefetch.2.10.7: 1) 'SRR063860' was downloaded successfully Read 29541264 spots for SRR063860/SRR063860.sra Written 29541264 spots for SRR063860/SRR063860.sra 2020-06-29T12:53:55 prefetch.2.10.7: 1) Downloading 'SRR063861'... 2020-06-29T12:53:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:55:50 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:55:51 prefetch.2.10.7: 'SRR063861' is valid 2020-06-29T12:55:51 prefetch.2.10.7: 1) 'SRR063861' was downloaded successfully Read 28799901 spots for SRR063861/SRR063861.sra Written 28799901 spots for SRR063861/SRR063861.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: 00:33:13 58341165 reads; of these: 58341165 (100.00%) were unpaired; of these: 3714334 (6.37%) aligned 0 times 18456085 (31.63%) aligned exactly 1 time 36170746 (62.00%) aligned >1 times 93.63% overall alignment rate Time searching: 00:33:13 Overall time: 00:33:13 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_sort_core] merging from 16 files... [bam_rmdupse_core] 37983386 / 54626831 = 0.6953 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 @ Mon, 29 Jun 2020 22:45:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.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 @ Mon, 29 Jun 2020 22:45:42: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:45:42: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:45:47: 1000000 INFO @ Mon, 29 Jun 2020 22:45:52: 2000000 INFO @ Mon, 29 Jun 2020 22:45:57: 3000000 INFO @ Mon, 29 Jun 2020 22:46:02: 4000000 INFO @ Mon, 29 Jun 2020 22:46:07: 5000000 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 @ Mon, 29 Jun 2020 22:46:12: 6000000 INFO @ Mon, 29 Jun 2020 22:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.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 @ Mon, 29 Jun 2020 22:46:12: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:46:12: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:46:17: 7000000 INFO @ Mon, 29 Jun 2020 22:46:18: 1000000 INFO @ Mon, 29 Jun 2020 22:46:22: 8000000 INFO @ Mon, 29 Jun 2020 22:46:23: 2000000 INFO @ Mon, 29 Jun 2020 22:46:28: 9000000 INFO @ Mon, 29 Jun 2020 22:46:28: 3000000 INFO @ Mon, 29 Jun 2020 22:46:34: 4000000 INFO @ Mon, 29 Jun 2020 22:46:34: 10000000 INFO @ Mon, 29 Jun 2020 22:46:39: 5000000 INFO @ Mon, 29 Jun 2020 22:46:40: 11000000 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 @ Mon, 29 Jun 2020 22:46:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.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 @ Mon, 29 Jun 2020 22:46:42: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:46:42: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:46:45: 6000000 INFO @ Mon, 29 Jun 2020 22:46:46: 12000000 INFO @ Mon, 29 Jun 2020 22:46:49: 1000000 INFO @ Mon, 29 Jun 2020 22:46:51: 7000000 INFO @ Mon, 29 Jun 2020 22:46:52: 13000000 INFO @ Mon, 29 Jun 2020 22:46:55: 2000000 INFO @ Mon, 29 Jun 2020 22:46:57: 8000000 INFO @ Mon, 29 Jun 2020 22:46:57: 14000000 INFO @ Mon, 29 Jun 2020 22:47:02: 3000000 INFO @ Mon, 29 Jun 2020 22:47:03: 9000000 INFO @ Mon, 29 Jun 2020 22:47:03: 15000000 INFO @ Mon, 29 Jun 2020 22:47:08: 4000000 INFO @ Mon, 29 Jun 2020 22:47:09: 16000000 INFO @ Mon, 29 Jun 2020 22:47:09: 10000000 INFO @ Mon, 29 Jun 2020 22:47:13: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:47:13: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:47:13: #1 total tags in treatment: 16643445 INFO @ Mon, 29 Jun 2020 22:47:13: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:47:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:47:13: #1 tags after filtering in treatment: 16643445 INFO @ Mon, 29 Jun 2020 22:47:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:47:13: #1 finished! INFO @ Mon, 29 Jun 2020 22:47:13: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:47:14: #2 number of paired peaks: 5965 INFO @ Mon, 29 Jun 2020 22:47:14: start model_add_line... INFO @ Mon, 29 Jun 2020 22:47:15: 5000000 INFO @ Mon, 29 Jun 2020 22:47:15: start X-correlation... INFO @ Mon, 29 Jun 2020 22:47:15: end of X-cor INFO @ Mon, 29 Jun 2020 22:47:15: #2 finished! INFO @ Mon, 29 Jun 2020 22:47:15: #2 predicted fragment length is 3 bps INFO @ Mon, 29 Jun 2020 22:47:15: #2 alternative fragment length(s) may be 3,17 bps INFO @ Mon, 29 Jun 2020 22:47:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.05_model.r WARNING @ Mon, 29 Jun 2020 22:47:15: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:47:15: #2 You may need to consider one of the other alternative d(s): 3,17 WARNING @ Mon, 29 Jun 2020 22:47:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:47:15: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:47:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:47:15: 11000000 INFO @ Mon, 29 Jun 2020 22:47:21: 6000000 INFO @ Mon, 29 Jun 2020 22:47:21: 12000000 INFO @ Mon, 29 Jun 2020 22:47:27: 13000000 INFO @ Mon, 29 Jun 2020 22:47:27: 7000000 INFO @ Mon, 29 Jun 2020 22:47:33: 14000000 INFO @ Mon, 29 Jun 2020 22:47:33: 8000000 INFO @ Mon, 29 Jun 2020 22:47:39: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:47:39: 15000000 INFO @ Mon, 29 Jun 2020 22:47:39: 9000000 INFO @ Mon, 29 Jun 2020 22:47:45: 16000000 INFO @ Mon, 29 Jun 2020 22:47:45: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:47:48: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:47:48: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:47:48: #1 total tags in treatment: 16643445 INFO @ Mon, 29 Jun 2020 22:47:48: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:47:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:47:49: #1 tags after filtering in treatment: 16643445 INFO @ Mon, 29 Jun 2020 22:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:47:49: #1 finished! INFO @ Mon, 29 Jun 2020 22:47:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.05_summits.bed INFO @ Mon, 29 Jun 2020 22:47:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:47:50: #2 number of paired peaks: 5965 INFO @ Mon, 29 Jun 2020 22:47:50: start model_add_line... INFO @ Mon, 29 Jun 2020 22:47:51: start X-correlation... INFO @ Mon, 29 Jun 2020 22:47:51: end of X-cor INFO @ Mon, 29 Jun 2020 22:47:51: #2 finished! INFO @ Mon, 29 Jun 2020 22:47:51: #2 predicted fragment length is 3 bps INFO @ Mon, 29 Jun 2020 22:47:51: #2 alternative fragment length(s) may be 3,17 bps INFO @ Mon, 29 Jun 2020 22:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.10_model.r WARNING @ Mon, 29 Jun 2020 22:47:51: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:47:51: #2 You may need to consider one of the other alternative d(s): 3,17 WARNING @ Mon, 29 Jun 2020 22:47:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:47:51: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:47:51: 11000000 INFO @ Mon, 29 Jun 2020 22:47:57: 12000000 INFO @ Mon, 29 Jun 2020 22:48:04: 13000000 INFO @ Mon, 29 Jun 2020 22:48:10: 14000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:48:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:48:16: 15000000 INFO @ Mon, 29 Jun 2020 22:48:22: 16000000 INFO @ Mon, 29 Jun 2020 22:48:25: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:48:25: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:48:25: #1 total tags in treatment: 16643445 INFO @ Mon, 29 Jun 2020 22:48:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:48:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:48:26: #1 tags after filtering in treatment: 16643445 INFO @ Mon, 29 Jun 2020 22:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:48:26: #1 finished! INFO @ Mon, 29 Jun 2020 22:48:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:48:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:48:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.10_summits.bed INFO @ Mon, 29 Jun 2020 22:48:26: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:48:27: #2 number of paired peaks: 5965 INFO @ Mon, 29 Jun 2020 22:48:27: start model_add_line... INFO @ Mon, 29 Jun 2020 22:48:28: start X-correlation... INFO @ Mon, 29 Jun 2020 22:48:28: end of X-cor INFO @ Mon, 29 Jun 2020 22:48:28: #2 finished! INFO @ Mon, 29 Jun 2020 22:48:28: #2 predicted fragment length is 3 bps INFO @ Mon, 29 Jun 2020 22:48:28: #2 alternative fragment length(s) may be 3,17 bps INFO @ Mon, 29 Jun 2020 22:48:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.20_model.r WARNING @ Mon, 29 Jun 2020 22:48:28: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:48:28: #2 You may need to consider one of the other alternative d(s): 3,17 WARNING @ Mon, 29 Jun 2020 22:48:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:48:28: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:48:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:48:51: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX025466/SRX025466.20_summits.bed INFO @ Mon, 29 Jun 2020 22:49:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling