Job ID = 6455862 SRX = SRX3020531 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:40:08 prefetch.2.10.7: 1) Downloading 'SRR5850384'... 2020-06-21T10:40:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:41:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:41:12 prefetch.2.10.7: 'SRR5850384' is valid 2020-06-21T10:41:12 prefetch.2.10.7: 1) 'SRR5850384' was downloaded successfully 2020-06-21T10:41:12 prefetch.2.10.7: 'SRR5850384' has 0 unresolved dependencies Read 5153948 spots for SRR5850384/SRR5850384.sra Written 5153948 spots for SRR5850384/SRR5850384.sra 2020-06-21T10:41:40 prefetch.2.10.7: 1) Downloading 'SRR5850385'... 2020-06-21T10:41:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:42:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:42:21 prefetch.2.10.7: 'SRR5850385' is valid 2020-06-21T10:42:21 prefetch.2.10.7: 1) 'SRR5850385' was downloaded successfully 2020-06-21T10:42:21 prefetch.2.10.7: 'SRR5850385' has 0 unresolved dependencies Read 5134730 spots for SRR5850385/SRR5850385.sra Written 5134730 spots for SRR5850385/SRR5850385.sra 2020-06-21T10:42:49 prefetch.2.10.7: 1) Downloading 'SRR5850386'... 2020-06-21T10:42:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:43:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:43:19 prefetch.2.10.7: 'SRR5850386' is valid 2020-06-21T10:43:19 prefetch.2.10.7: 1) 'SRR5850386' was downloaded successfully 2020-06-21T10:43:19 prefetch.2.10.7: 'SRR5850386' has 0 unresolved dependencies Read 5080066 spots for SRR5850386/SRR5850386.sra Written 5080066 spots for SRR5850386/SRR5850386.sra 2020-06-21T10:43:46 prefetch.2.10.7: 1) Downloading 'SRR5850387'... 2020-06-21T10:43:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:44:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:44:58 prefetch.2.10.7: 'SRR5850387' is valid 2020-06-21T10:44:58 prefetch.2.10.7: 1) 'SRR5850387' was downloaded successfully 2020-06-21T10:44:58 prefetch.2.10.7: 'SRR5850387' has 0 unresolved dependencies Read 5062025 spots for SRR5850387/SRR5850387.sra Written 5062025 spots for SRR5850387/SRR5850387.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: 00:05:42 20430769 reads; of these: 20430769 (100.00%) were unpaired; of these: 841798 (4.12%) aligned 0 times 14073660 (68.88%) aligned exactly 1 time 5515311 (27.00%) aligned >1 times 95.88% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 2894066 / 19588971 = 0.1477 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 19:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.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 19:55:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:03: 1000000 INFO @ Sun, 21 Jun 2020 19:56:09: 2000000 INFO @ Sun, 21 Jun 2020 19:56:15: 3000000 INFO @ Sun, 21 Jun 2020 19:56:22: 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 19:56:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.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 19:56:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:28: 5000000 INFO @ Sun, 21 Jun 2020 19:56:33: 1000000 INFO @ Sun, 21 Jun 2020 19:56:35: 6000000 INFO @ Sun, 21 Jun 2020 19:56:39: 2000000 INFO @ Sun, 21 Jun 2020 19:56:41: 7000000 INFO @ Sun, 21 Jun 2020 19:56:45: 3000000 INFO @ Sun, 21 Jun 2020 19:56:48: 8000000 INFO @ Sun, 21 Jun 2020 19:56:51: 4000000 INFO @ Sun, 21 Jun 2020 19:56:54: 9000000 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 19:56:56: 5000000 INFO @ Sun, 21 Jun 2020 19:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.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 19:56:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:01: 10000000 INFO @ Sun, 21 Jun 2020 19:57:02: 6000000 INFO @ Sun, 21 Jun 2020 19:57:04: 1000000 INFO @ Sun, 21 Jun 2020 19:57:07: 11000000 INFO @ Sun, 21 Jun 2020 19:57:08: 7000000 INFO @ Sun, 21 Jun 2020 19:57:11: 2000000 INFO @ Sun, 21 Jun 2020 19:57:14: 12000000 INFO @ Sun, 21 Jun 2020 19:57:14: 8000000 INFO @ Sun, 21 Jun 2020 19:57:17: 3000000 INFO @ Sun, 21 Jun 2020 19:57:20: 9000000 INFO @ Sun, 21 Jun 2020 19:57:20: 13000000 INFO @ Sun, 21 Jun 2020 19:57:24: 4000000 INFO @ Sun, 21 Jun 2020 19:57:26: 10000000 INFO @ Sun, 21 Jun 2020 19:57:27: 14000000 INFO @ Sun, 21 Jun 2020 19:57:31: 5000000 INFO @ Sun, 21 Jun 2020 19:57:32: 11000000 INFO @ Sun, 21 Jun 2020 19:57:34: 15000000 INFO @ Sun, 21 Jun 2020 19:57:37: 6000000 INFO @ Sun, 21 Jun 2020 19:57:38: 12000000 INFO @ Sun, 21 Jun 2020 19:57:40: 16000000 INFO @ Sun, 21 Jun 2020 19:57:44: 13000000 INFO @ Sun, 21 Jun 2020 19:57:44: 7000000 INFO @ Sun, 21 Jun 2020 19:57:45: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:57:45: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:57:45: #1 total tags in treatment: 16694905 INFO @ Sun, 21 Jun 2020 19:57:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:45: #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 19:57:45: #1 tags after filtering in treatment: 16694827 INFO @ Sun, 21 Jun 2020 19:57:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:46: #2 number of paired peaks: 1232 INFO @ Sun, 21 Jun 2020 19:57:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:47: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:57:47: #2 alternative fragment length(s) may be 2,54 bps INFO @ Sun, 21 Jun 2020 19:57:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.05_model.r WARNING @ Sun, 21 Jun 2020 19:57:47: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:47: #2 You may need to consider one of the other alternative d(s): 2,54 WARNING @ Sun, 21 Jun 2020 19:57:47: #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 19:57:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:50: 14000000 INFO @ Sun, 21 Jun 2020 19:57:50: 8000000 INFO @ Sun, 21 Jun 2020 19:57:56: 15000000 INFO @ Sun, 21 Jun 2020 19:57:57: 9000000 INFO @ Sun, 21 Jun 2020 19:58:01: 16000000 INFO @ Sun, 21 Jun 2020 19:58:03: 10000000 INFO @ Sun, 21 Jun 2020 19:58:06: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:58:06: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:58:06: #1 total tags in treatment: 16694905 INFO @ Sun, 21 Jun 2020 19:58:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:06: #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 19:58:06: #1 tags after filtering in treatment: 16694827 INFO @ Sun, 21 Jun 2020 19:58:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:07: #2 number of paired peaks: 1232 INFO @ Sun, 21 Jun 2020 19:58:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:07: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:58:07: #2 alternative fragment length(s) may be 2,54 bps INFO @ Sun, 21 Jun 2020 19:58:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.10_model.r WARNING @ Sun, 21 Jun 2020 19:58:07: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:58:07: #2 You may need to consider one of the other alternative d(s): 2,54 WARNING @ Sun, 21 Jun 2020 19:58:07: #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 19:58:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:10: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:58:16: 12000000 INFO @ Sun, 21 Jun 2020 19:58:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:22: 13000000 INFO @ Sun, 21 Jun 2020 19:58:29: 14000000 INFO @ Sun, 21 Jun 2020 19:58:35: 15000000 INFO @ Sun, 21 Jun 2020 19:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.05_summits.bed INFO @ Sun, 21 Jun 2020 19:58:35: Done! pass1 - making usageList (632 chroms): 1 millis pass2 - checking and writing primary data (4122 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:58:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:41: 16000000 INFO @ Sun, 21 Jun 2020 19:58:45: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 19:58:45: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 19:58:45: #1 total tags in treatment: 16694905 INFO @ Sun, 21 Jun 2020 19:58:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:45: #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 19:58:46: #1 tags after filtering in treatment: 16694827 INFO @ Sun, 21 Jun 2020 19:58:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:46: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:58:47: #2 number of paired peaks: 1232 INFO @ Sun, 21 Jun 2020 19:58:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:47: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 19:58:47: #2 alternative fragment length(s) may be 2,54 bps INFO @ Sun, 21 Jun 2020 19:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.20_model.r WARNING @ Sun, 21 Jun 2020 19:58:47: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:58:47: #2 You may need to consider one of the other alternative d(s): 2,54 WARNING @ Sun, 21 Jun 2020 19:58:47: #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 19:58:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.10_summits.bed INFO @ Sun, 21 Jun 2020 19:58:55: Done! pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (2082 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:59:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020531/SRX3020531.20_summits.bed INFO @ Sun, 21 Jun 2020 19:59:35: Done! pass1 - making usageList (276 chroms): 1 millis pass2 - checking and writing primary data (689 records, 4 fields): 9 millis CompletedMACS2peakCalling