Job ID = 6498751 SRX = SRX750074 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:53:48 prefetch.2.10.7: 1) Downloading 'SRR1638760'... 2020-06-25T23:53:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:56:39 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:56:39 prefetch.2.10.7: 1) 'SRR1638760' was downloaded successfully Read 21475631 spots for SRR1638760/SRR1638760.sra Written 21475631 spots for SRR1638760/SRR1638760.sra 2020-06-25T23:58:00 prefetch.2.10.7: 1) Downloading 'SRR1638761'... 2020-06-25T23:58:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:01:14 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:01:14 prefetch.2.10.7: 1) 'SRR1638761' was downloaded successfully Read 18992466 spots for SRR1638761/SRR1638761.sra Written 18992466 spots for SRR1638761/SRR1638761.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: 00:16:03 40468097 reads; of these: 40468097 (100.00%) were unpaired; of these: 4361298 (10.78%) aligned 0 times 29338646 (72.50%) aligned exactly 1 time 6768153 (16.72%) aligned >1 times 89.22% overall alignment rate Time searching: 00:16:03 Overall time: 00:16:03 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] 28017816 / 36106799 = 0.7760 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 09:26:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.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 09:26:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:26:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:26:58: 1000000 INFO @ Fri, 26 Jun 2020 09:27:04: 2000000 INFO @ Fri, 26 Jun 2020 09:27:10: 3000000 INFO @ Fri, 26 Jun 2020 09:27:16: 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 09:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.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 09:27:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:27:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:27:22: 5000000 INFO @ Fri, 26 Jun 2020 09:27:28: 1000000 INFO @ Fri, 26 Jun 2020 09:27:28: 6000000 INFO @ Fri, 26 Jun 2020 09:27:34: 2000000 INFO @ Fri, 26 Jun 2020 09:27:34: 7000000 INFO @ Fri, 26 Jun 2020 09:27:40: 3000000 INFO @ Fri, 26 Jun 2020 09:27:40: 8000000 INFO @ Fri, 26 Jun 2020 09:27:41: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:27:41: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:27:41: #1 total tags in treatment: 8088983 INFO @ Fri, 26 Jun 2020 09:27:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:27:41: #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 09:27:41: #1 tags after filtering in treatment: 8088983 INFO @ Fri, 26 Jun 2020 09:27:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:27:41: #1 finished! INFO @ Fri, 26 Jun 2020 09:27:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:27:42: #2 number of paired peaks: 5496 INFO @ Fri, 26 Jun 2020 09:27:42: start model_add_line... INFO @ Fri, 26 Jun 2020 09:27:42: start X-correlation... INFO @ Fri, 26 Jun 2020 09:27:42: end of X-cor INFO @ Fri, 26 Jun 2020 09:27:42: #2 finished! INFO @ Fri, 26 Jun 2020 09:27:42: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 09:27:42: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 26 Jun 2020 09:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.05_model.r WARNING @ Fri, 26 Jun 2020 09:27:42: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:27:42: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Fri, 26 Jun 2020 09:27:42: #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 09:27:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:27:46: 4000000 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 09:27:52: 5000000 INFO @ Fri, 26 Jun 2020 09:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.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 09:27:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:27:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:27:58: 6000000 INFO @ Fri, 26 Jun 2020 09:27:59: 1000000 INFO @ Fri, 26 Jun 2020 09:28:04: 7000000 INFO @ Fri, 26 Jun 2020 09:28:06: 2000000 INFO @ Fri, 26 Jun 2020 09:28:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:28:10: 8000000 INFO @ Fri, 26 Jun 2020 09:28:11: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:28:11: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:28:11: #1 total tags in treatment: 8088983 INFO @ Fri, 26 Jun 2020 09:28:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:28:11: #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 09:28:11: #1 tags after filtering in treatment: 8088983 INFO @ Fri, 26 Jun 2020 09:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:28:11: #1 finished! INFO @ Fri, 26 Jun 2020 09:28:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:28:12: #2 number of paired peaks: 5496 INFO @ Fri, 26 Jun 2020 09:28:12: start model_add_line... INFO @ Fri, 26 Jun 2020 09:28:12: start X-correlation... INFO @ Fri, 26 Jun 2020 09:28:12: end of X-cor INFO @ Fri, 26 Jun 2020 09:28:12: #2 finished! INFO @ Fri, 26 Jun 2020 09:28:12: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 09:28:12: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 26 Jun 2020 09:28:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.10_model.r WARNING @ Fri, 26 Jun 2020 09:28:12: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:28:12: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Fri, 26 Jun 2020 09:28:12: #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 09:28:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:28:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:28:13: 3000000 INFO @ Fri, 26 Jun 2020 09:28:20: 4000000 INFO @ Fri, 26 Jun 2020 09:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.05_summits.bed INFO @ Fri, 26 Jun 2020 09:28:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6970 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:28:27: 5000000 INFO @ Fri, 26 Jun 2020 09:28:34: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:28:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:28:41: 7000000 INFO @ Fri, 26 Jun 2020 09:28:47: 8000000 INFO @ Fri, 26 Jun 2020 09:28:48: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:28:48: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:28:48: #1 total tags in treatment: 8088983 INFO @ Fri, 26 Jun 2020 09:28:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:28:48: #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 09:28:48: #1 tags after filtering in treatment: 8088983 INFO @ Fri, 26 Jun 2020 09:28:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:28:48: #1 finished! INFO @ Fri, 26 Jun 2020 09:28:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:28:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:28:49: #2 number of paired peaks: 5496 INFO @ Fri, 26 Jun 2020 09:28:49: start model_add_line... INFO @ Fri, 26 Jun 2020 09:28:49: start X-correlation... INFO @ Fri, 26 Jun 2020 09:28:49: end of X-cor INFO @ Fri, 26 Jun 2020 09:28:49: #2 finished! INFO @ Fri, 26 Jun 2020 09:28:49: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 09:28:49: #2 alternative fragment length(s) may be 125 bps INFO @ Fri, 26 Jun 2020 09:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.20_model.r WARNING @ Fri, 26 Jun 2020 09:28:49: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:28:49: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Fri, 26 Jun 2020 09:28:49: #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 09:28:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:28:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:28:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:28:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.10_summits.bed INFO @ Fri, 26 Jun 2020 09:28:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5030 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:29:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:29:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:29:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:29:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750074/SRX750074.20_summits.bed INFO @ Fri, 26 Jun 2020 09:29:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3362 records, 4 fields): 6 millis CompletedMACS2peakCalling