Job ID = 6457941 SRX = SRX4923185 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:18:38 prefetch.2.10.7: 1) Downloading 'SRR8096335'... 2020-06-21T12:18:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:40 prefetch.2.10.7: 'SRR8096335' is valid 2020-06-21T12:20:40 prefetch.2.10.7: 1) 'SRR8096335' was downloaded successfully 2020-06-21T12:20:40 prefetch.2.10.7: 'SRR8096335' has 0 unresolved dependencies Read 19809513 spots for SRR8096335/SRR8096335.sra Written 19809513 spots for SRR8096335/SRR8096335.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: 00:07:15 19809513 reads; of these: 19809513 (100.00%) were unpaired; of these: 443903 (2.24%) aligned 0 times 5814254 (29.35%) aligned exactly 1 time 13551356 (68.41%) aligned >1 times 97.76% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 8187877 / 19365610 = 0.4228 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 21:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.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 21:33:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:21: 1000000 INFO @ Sun, 21 Jun 2020 21:33:25: 2000000 INFO @ Sun, 21 Jun 2020 21:33:30: 3000000 INFO @ Sun, 21 Jun 2020 21:33:35: 4000000 INFO @ Sun, 21 Jun 2020 21:33:40: 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 @ Sun, 21 Jun 2020 21:33:45: 6000000 INFO @ Sun, 21 Jun 2020 21:33:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.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 21:33:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:50: 7000000 INFO @ Sun, 21 Jun 2020 21:33:51: 1000000 INFO @ Sun, 21 Jun 2020 21:33:55: 8000000 INFO @ Sun, 21 Jun 2020 21:33:56: 2000000 INFO @ Sun, 21 Jun 2020 21:34:00: 9000000 INFO @ Sun, 21 Jun 2020 21:34:00: 3000000 INFO @ Sun, 21 Jun 2020 21:34:05: 10000000 INFO @ Sun, 21 Jun 2020 21:34:05: 4000000 INFO @ Sun, 21 Jun 2020 21:34:10: 5000000 INFO @ Sun, 21 Jun 2020 21:34:10: 11000000 INFO @ Sun, 21 Jun 2020 21:34:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:34:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:34:11: #1 total tags in treatment: 11177733 INFO @ Sun, 21 Jun 2020 21:34:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:11: #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 21:34:12: #1 tags after filtering in treatment: 11177671 INFO @ Sun, 21 Jun 2020 21:34:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:12: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:12: #2 looking for paired plus/minus strand peaks... 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 21:34:14: #2 number of paired peaks: 6856 INFO @ Sun, 21 Jun 2020 21:34:14: start model_add_line... INFO @ Sun, 21 Jun 2020 21:34:14: start X-correlation... INFO @ Sun, 21 Jun 2020 21:34:14: end of X-cor INFO @ Sun, 21 Jun 2020 21:34:14: #2 finished! INFO @ Sun, 21 Jun 2020 21:34:14: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 21:34:14: #2 alternative fragment length(s) may be 3,84 bps INFO @ Sun, 21 Jun 2020 21:34:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.05_model.r WARNING @ Sun, 21 Jun 2020 21:34:14: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:34:14: #2 You may need to consider one of the other alternative d(s): 3,84 WARNING @ Sun, 21 Jun 2020 21:34:14: #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 21:34:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:34:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:15: 6000000 INFO @ Sun, 21 Jun 2020 21:34:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.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 21:34:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:20: 7000000 INFO @ Sun, 21 Jun 2020 21:34:21: 1000000 INFO @ Sun, 21 Jun 2020 21:34:25: 8000000 INFO @ Sun, 21 Jun 2020 21:34:26: 2000000 INFO @ Sun, 21 Jun 2020 21:34:30: 9000000 INFO @ Sun, 21 Jun 2020 21:34:31: 3000000 INFO @ Sun, 21 Jun 2020 21:34:35: 10000000 INFO @ Sun, 21 Jun 2020 21:34:36: 4000000 INFO @ Sun, 21 Jun 2020 21:34:40: 11000000 INFO @ Sun, 21 Jun 2020 21:34:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:34:41: 5000000 INFO @ Sun, 21 Jun 2020 21:34:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:34:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:34:41: #1 total tags in treatment: 11177733 INFO @ Sun, 21 Jun 2020 21:34:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:41: #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 21:34:42: #1 tags after filtering in treatment: 11177671 INFO @ Sun, 21 Jun 2020 21:34:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:34:44: #2 number of paired peaks: 6856 INFO @ Sun, 21 Jun 2020 21:34:44: start model_add_line... INFO @ Sun, 21 Jun 2020 21:34:44: start X-correlation... INFO @ Sun, 21 Jun 2020 21:34:44: end of X-cor INFO @ Sun, 21 Jun 2020 21:34:44: #2 finished! INFO @ Sun, 21 Jun 2020 21:34:44: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 21:34:44: #2 alternative fragment length(s) may be 3,84 bps INFO @ Sun, 21 Jun 2020 21:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.10_model.r WARNING @ Sun, 21 Jun 2020 21:34:44: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:34:44: #2 You may need to consider one of the other alternative d(s): 3,84 WARNING @ Sun, 21 Jun 2020 21:34:44: #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 21:34:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:46: 6000000 INFO @ Sun, 21 Jun 2020 21:34:51: 7000000 INFO @ Sun, 21 Jun 2020 21:34:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:34:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:34:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.05_summits.bed INFO @ Sun, 21 Jun 2020 21:34:53: Done! pass1 - making usageList (1061 chroms): 3 millis pass2 - checking and writing primary data (8120 records, 4 fields): 65 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:34:57: 8000000 INFO @ Sun, 21 Jun 2020 21:35:02: 9000000 INFO @ Sun, 21 Jun 2020 21:35:07: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:35:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:12: 11000000 INFO @ Sun, 21 Jun 2020 21:35:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:13: #1 total tags in treatment: 11177733 INFO @ Sun, 21 Jun 2020 21:35:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:13: #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 21:35:14: #1 tags after filtering in treatment: 11177671 INFO @ Sun, 21 Jun 2020 21:35:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:14: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:15: #2 number of paired peaks: 6856 INFO @ Sun, 21 Jun 2020 21:35:15: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:15: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:15: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:15: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:15: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 21:35:15: #2 alternative fragment length(s) may be 3,84 bps INFO @ Sun, 21 Jun 2020 21:35:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.20_model.r WARNING @ Sun, 21 Jun 2020 21:35:15: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:15: #2 You may need to consider one of the other alternative d(s): 3,84 WARNING @ Sun, 21 Jun 2020 21:35:15: #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 21:35:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.10_summits.bed INFO @ Sun, 21 Jun 2020 21:35:21: Done! pass1 - making usageList (949 chroms): 2 millis pass2 - checking and writing primary data (4159 records, 4 fields): 54 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:35:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923185/SRX4923185.20_summits.bed INFO @ Sun, 21 Jun 2020 21:35:53: Done! pass1 - making usageList (717 chroms): 2 millis pass2 - checking and writing primary data (2031 records, 4 fields): 40 millis CompletedMACS2peakCalling