Job ID = 6458415 SRX = SRX5226974 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:37 prefetch.2.10.7: 1) Downloading 'SRR8417889'... 2020-06-21T12:30:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:32:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:32:15 prefetch.2.10.7: 'SRR8417889' is valid 2020-06-21T12:32:15 prefetch.2.10.7: 1) 'SRR8417889' was downloaded successfully 2020-06-21T12:32:15 prefetch.2.10.7: 'SRR8417889' has 0 unresolved dependencies Read 12127246 spots for SRR8417889/SRR8417889.sra Written 12127246 spots for SRR8417889/SRR8417889.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: 00:04:45 12127246 reads; of these: 12127246 (100.00%) were unpaired; of these: 1187546 (9.79%) aligned 0 times 7694123 (63.44%) aligned exactly 1 time 3245577 (26.76%) aligned >1 times 90.21% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 1337793 / 10939700 = 0.1223 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 21:41:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.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 21:41:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:59: 1000000 INFO @ Sun, 21 Jun 2020 21:42:05: 2000000 INFO @ Sun, 21 Jun 2020 21:42:11: 3000000 INFO @ Sun, 21 Jun 2020 21:42:17: 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 @ Sun, 21 Jun 2020 21:42:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.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 21:42:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:24: 5000000 INFO @ Sun, 21 Jun 2020 21:42:29: 1000000 INFO @ Sun, 21 Jun 2020 21:42:30: 6000000 INFO @ Sun, 21 Jun 2020 21:42:35: 2000000 INFO @ Sun, 21 Jun 2020 21:42:37: 7000000 INFO @ Sun, 21 Jun 2020 21:42:42: 3000000 INFO @ Sun, 21 Jun 2020 21:42:44: 8000000 INFO @ Sun, 21 Jun 2020 21:42:49: 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 @ Sun, 21 Jun 2020 21:42:51: 9000000 INFO @ Sun, 21 Jun 2020 21:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.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 21:42:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:55: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:42:55: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:42:55: #1 total tags in treatment: 9601907 INFO @ Sun, 21 Jun 2020 21:42:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:55: #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 21:42:56: #1 tags after filtering in treatment: 9601739 INFO @ Sun, 21 Jun 2020 21:42:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:56: 5000000 INFO @ Sun, 21 Jun 2020 21:42:57: #2 number of paired peaks: 1540 INFO @ Sun, 21 Jun 2020 21:42:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:57: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 21:42:57: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 21:42:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.05_model.r WARNING @ Sun, 21 Jun 2020 21:42:57: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:42:57: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 21:42:57: #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 21:42:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:59: 1000000 INFO @ Sun, 21 Jun 2020 21:43:03: 6000000 INFO @ Sun, 21 Jun 2020 21:43:05: 2000000 INFO @ Sun, 21 Jun 2020 21:43:10: 7000000 INFO @ Sun, 21 Jun 2020 21:43:11: 3000000 INFO @ Sun, 21 Jun 2020 21:43:16: 8000000 INFO @ Sun, 21 Jun 2020 21:43:17: 4000000 INFO @ Sun, 21 Jun 2020 21:43:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:23: 9000000 INFO @ Sun, 21 Jun 2020 21:43:24: 5000000 INFO @ Sun, 21 Jun 2020 21:43:28: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:43:28: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:43:28: #1 total tags in treatment: 9601907 INFO @ Sun, 21 Jun 2020 21:43:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:28: #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 21:43:28: #1 tags after filtering in treatment: 9601739 INFO @ Sun, 21 Jun 2020 21:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:29: #2 number of paired peaks: 1540 INFO @ Sun, 21 Jun 2020 21:43:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:29: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:29: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:29: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:29: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 21:43:29: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 21:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.10_model.r WARNING @ Sun, 21 Jun 2020 21:43:29: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:29: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 21:43:29: #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 21:43:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:43:30: 6000000 INFO @ Sun, 21 Jun 2020 21:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.05_summits.bed INFO @ Sun, 21 Jun 2020 21:43:31: Done! pass1 - making usageList (530 chroms): 2 millis pass2 - checking and writing primary data (3403 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:43:36: 7000000 INFO @ Sun, 21 Jun 2020 21:43:42: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:43:48: 9000000 INFO @ Sun, 21 Jun 2020 21:43:52: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:43:52: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:43:52: #1 total tags in treatment: 9601907 INFO @ Sun, 21 Jun 2020 21:43:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:52: #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 21:43:53: #1 tags after filtering in treatment: 9601739 INFO @ Sun, 21 Jun 2020 21:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:53: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:53: #2 number of paired peaks: 1540 INFO @ Sun, 21 Jun 2020 21:43:53: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:53: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:53: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:53: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:53: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 21:43:53: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 21:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.20_model.r WARNING @ Sun, 21 Jun 2020 21:43:53: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:53: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 21:43:53: #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 21:43:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.10_summits.bed INFO @ Sun, 21 Jun 2020 21:44:05: Done! pass1 - making usageList (350 chroms): 1 millis pass2 - checking and writing primary data (1693 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:44:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:44:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226974/SRX5226974.20_summits.bed INFO @ Sun, 21 Jun 2020 21:44:30: Done! pass1 - making usageList (195 chroms): 1 millis pass2 - checking and writing primary data (648 records, 4 fields): 7 millis CompletedMACS2peakCalling