Job ID = 6498301 SRX = SRX467112 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:34:30 prefetch.2.10.7: 1) Downloading 'SRR1164536'... 2020-06-25T23:34:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:36:30 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:36:31 prefetch.2.10.7: 'SRR1164536' is valid 2020-06-25T23:36:31 prefetch.2.10.7: 1) 'SRR1164536' was downloaded successfully Read 14698347 spots for SRR1164536/SRR1164536.sra Written 14698347 spots for SRR1164536/SRR1164536.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: 00:05:46 14698347 reads; of these: 14698347 (100.00%) were unpaired; of these: 870150 (5.92%) aligned 0 times 8935571 (60.79%) aligned exactly 1 time 4892626 (33.29%) aligned >1 times 94.08% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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 8 files... [bam_rmdupse_core] 1150934 / 13828197 = 0.0832 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 08:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.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 08:47:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:47:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:47:23: 1000000 INFO @ Fri, 26 Jun 2020 08:47:29: 2000000 INFO @ Fri, 26 Jun 2020 08:47:36: 3000000 INFO @ Fri, 26 Jun 2020 08:47:42: 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 08:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.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 08:47:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:47:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:47:49: 5000000 INFO @ Fri, 26 Jun 2020 08:47:53: 1000000 INFO @ Fri, 26 Jun 2020 08:47:57: 6000000 INFO @ Fri, 26 Jun 2020 08:48:01: 2000000 INFO @ Fri, 26 Jun 2020 08:48:04: 7000000 INFO @ Fri, 26 Jun 2020 08:48:08: 3000000 INFO @ Fri, 26 Jun 2020 08:48:11: 8000000 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 08:48:15: 4000000 INFO @ Fri, 26 Jun 2020 08:48:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.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 08:48:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:48:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:48:19: 9000000 INFO @ Fri, 26 Jun 2020 08:48:24: 5000000 INFO @ Fri, 26 Jun 2020 08:48:25: 1000000 INFO @ Fri, 26 Jun 2020 08:48:27: 10000000 INFO @ Fri, 26 Jun 2020 08:48:32: 6000000 INFO @ Fri, 26 Jun 2020 08:48:34: 2000000 INFO @ Fri, 26 Jun 2020 08:48:35: 11000000 INFO @ Fri, 26 Jun 2020 08:48:40: 7000000 INFO @ Fri, 26 Jun 2020 08:48:43: 3000000 INFO @ Fri, 26 Jun 2020 08:48:43: 12000000 INFO @ Fri, 26 Jun 2020 08:48:48: 8000000 INFO @ Fri, 26 Jun 2020 08:48:49: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:48:49: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:48:49: #1 total tags in treatment: 12677263 INFO @ Fri, 26 Jun 2020 08:48:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:48:49: #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 08:48:49: #1 tags after filtering in treatment: 12677263 INFO @ Fri, 26 Jun 2020 08:48:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:48:49: #1 finished! INFO @ Fri, 26 Jun 2020 08:48:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:48:50: #2 number of paired peaks: 1053 INFO @ Fri, 26 Jun 2020 08:48:50: start model_add_line... INFO @ Fri, 26 Jun 2020 08:48:50: start X-correlation... INFO @ Fri, 26 Jun 2020 08:48:50: end of X-cor INFO @ Fri, 26 Jun 2020 08:48:50: #2 finished! INFO @ Fri, 26 Jun 2020 08:48:50: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 08:48:50: #2 alternative fragment length(s) may be 3,49 bps INFO @ Fri, 26 Jun 2020 08:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.05_model.r WARNING @ Fri, 26 Jun 2020 08:48:50: #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 08:48:50: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Fri, 26 Jun 2020 08:48:50: #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 08:48:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:48:52: 4000000 INFO @ Fri, 26 Jun 2020 08:48:56: 9000000 INFO @ Fri, 26 Jun 2020 08:49:01: 5000000 INFO @ Fri, 26 Jun 2020 08:49:04: 10000000 INFO @ Fri, 26 Jun 2020 08:49:09: 6000000 INFO @ Fri, 26 Jun 2020 08:49:13: 11000000 INFO @ Fri, 26 Jun 2020 08:49:18: 7000000 INFO @ Fri, 26 Jun 2020 08:49:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:49:21: 12000000 INFO @ Fri, 26 Jun 2020 08:49:26: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:49:26: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:49:26: #1 total tags in treatment: 12677263 INFO @ Fri, 26 Jun 2020 08:49:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:49:26: #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 08:49:26: #1 tags after filtering in treatment: 12677263 INFO @ Fri, 26 Jun 2020 08:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:49:26: #1 finished! INFO @ Fri, 26 Jun 2020 08:49:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:49:27: 8000000 INFO @ Fri, 26 Jun 2020 08:49:27: #2 number of paired peaks: 1053 INFO @ Fri, 26 Jun 2020 08:49:27: start model_add_line... INFO @ Fri, 26 Jun 2020 08:49:27: start X-correlation... INFO @ Fri, 26 Jun 2020 08:49:27: end of X-cor INFO @ Fri, 26 Jun 2020 08:49:27: #2 finished! INFO @ Fri, 26 Jun 2020 08:49:27: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 08:49:27: #2 alternative fragment length(s) may be 3,49 bps INFO @ Fri, 26 Jun 2020 08:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.10_model.r WARNING @ Fri, 26 Jun 2020 08:49:28: #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 08:49:28: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Fri, 26 Jun 2020 08:49:28: #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 08:49:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:49:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:49:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:49:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.05_summits.bed INFO @ Fri, 26 Jun 2020 08:49:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3463 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:49:35: 9000000 INFO @ Fri, 26 Jun 2020 08:49:43: 10000000 INFO @ Fri, 26 Jun 2020 08:49:50: 11000000 INFO @ Fri, 26 Jun 2020 08:49:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:49:58: 12000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:50:04: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:50:04: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:50:04: #1 total tags in treatment: 12677263 INFO @ Fri, 26 Jun 2020 08:50:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:50:04: #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 08:50:04: #1 tags after filtering in treatment: 12677263 INFO @ Fri, 26 Jun 2020 08:50:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:50:04: #1 finished! INFO @ Fri, 26 Jun 2020 08:50:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:50:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:50:05: #2 number of paired peaks: 1053 INFO @ Fri, 26 Jun 2020 08:50:05: start model_add_line... INFO @ Fri, 26 Jun 2020 08:50:05: start X-correlation... INFO @ Fri, 26 Jun 2020 08:50:05: end of X-cor INFO @ Fri, 26 Jun 2020 08:50:05: #2 finished! INFO @ Fri, 26 Jun 2020 08:50:05: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 08:50:05: #2 alternative fragment length(s) may be 3,49 bps INFO @ Fri, 26 Jun 2020 08:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.20_model.r WARNING @ Fri, 26 Jun 2020 08:50:05: #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 08:50:05: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Fri, 26 Jun 2020 08:50:05: #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 08:50:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:50:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:50:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:50:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.10_summits.bed INFO @ Fri, 26 Jun 2020 08:50:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2325 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:50:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:50:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:50:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:50:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467112/SRX467112.20_summits.bed INFO @ Fri, 26 Jun 2020 08:50:47: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (927 records, 4 fields): 2 millis CompletedMACS2peakCalling