Job ID = 6457935 SRX = SRX4923181 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:00:35 prefetch.2.10.7: 1) Downloading 'SRR8096331'... 2020-06-21T12:00:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:02:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:02:58 prefetch.2.10.7: 'SRR8096331' is valid 2020-06-21T12:02:58 prefetch.2.10.7: 1) 'SRR8096331' was downloaded successfully 2020-06-21T12:02:58 prefetch.2.10.7: 'SRR8096331' has 0 unresolved dependencies Read 22966947 spots for SRR8096331/SRR8096331.sra Written 22966947 spots for SRR8096331/SRR8096331.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: 00:08:03 22966947 reads; of these: 22966947 (100.00%) were unpaired; of these: 557110 (2.43%) aligned 0 times 6986244 (30.42%) aligned exactly 1 time 15423593 (67.16%) aligned >1 times 97.57% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9509901 / 22409837 = 0.4244 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 21:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.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 21:16:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:16:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:16:05: 1000000 INFO @ Sun, 21 Jun 2020 21:16:10: 2000000 INFO @ Sun, 21 Jun 2020 21:16:16: 3000000 INFO @ Sun, 21 Jun 2020 21:16:21: 4000000 INFO @ Sun, 21 Jun 2020 21:16:26: 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 21:16:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.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 21:16:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:16:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:16:31: 6000000 INFO @ Sun, 21 Jun 2020 21:16:35: 1000000 INFO @ Sun, 21 Jun 2020 21:16:37: 7000000 INFO @ Sun, 21 Jun 2020 21:16:40: 2000000 INFO @ Sun, 21 Jun 2020 21:16:42: 8000000 INFO @ Sun, 21 Jun 2020 21:16:46: 3000000 INFO @ Sun, 21 Jun 2020 21:16:48: 9000000 INFO @ Sun, 21 Jun 2020 21:16:51: 4000000 INFO @ Sun, 21 Jun 2020 21:16:53: 10000000 INFO @ Sun, 21 Jun 2020 21:16:57: 5000000 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 21:16:59: 11000000 INFO @ Sun, 21 Jun 2020 21:17:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.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 21:17:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:17:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:17:03: 6000000 INFO @ Sun, 21 Jun 2020 21:17:04: 12000000 INFO @ Sun, 21 Jun 2020 21:17:06: 1000000 INFO @ Sun, 21 Jun 2020 21:17:08: 7000000 INFO @ Sun, 21 Jun 2020 21:17:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:17:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:17:09: #1 total tags in treatment: 12899936 INFO @ Sun, 21 Jun 2020 21:17:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:09: #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 21:17:10: #1 tags after filtering in treatment: 12899884 INFO @ Sun, 21 Jun 2020 21:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:11: #2 number of paired peaks: 6578 INFO @ Sun, 21 Jun 2020 21:17:11: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:11: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:11: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:11: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:11: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:17:11: #2 alternative fragment length(s) may be 3,72 bps INFO @ Sun, 21 Jun 2020 21:17:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.05_model.r WARNING @ Sun, 21 Jun 2020 21:17:11: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:17:11: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Sun, 21 Jun 2020 21:17:11: #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 21:17:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:17:11: 2000000 INFO @ Sun, 21 Jun 2020 21:17:14: 8000000 INFO @ Sun, 21 Jun 2020 21:17:17: 3000000 INFO @ Sun, 21 Jun 2020 21:17:19: 9000000 INFO @ Sun, 21 Jun 2020 21:17:22: 4000000 INFO @ Sun, 21 Jun 2020 21:17:25: 10000000 INFO @ Sun, 21 Jun 2020 21:17:28: 5000000 INFO @ Sun, 21 Jun 2020 21:17:31: 11000000 INFO @ Sun, 21 Jun 2020 21:17:33: 6000000 INFO @ Sun, 21 Jun 2020 21:17:36: 12000000 INFO @ Sun, 21 Jun 2020 21:17:39: 7000000 INFO @ Sun, 21 Jun 2020 21:17:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:17:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:17:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:17:41: #1 total tags in treatment: 12899936 INFO @ Sun, 21 Jun 2020 21:17:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:17:41: #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 21:17:42: #1 tags after filtering in treatment: 12899884 INFO @ Sun, 21 Jun 2020 21:17:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:17:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:17:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:17:43: #2 number of paired peaks: 6578 INFO @ Sun, 21 Jun 2020 21:17:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:17:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:17:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:17:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:17:43: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:17:43: #2 alternative fragment length(s) may be 3,72 bps INFO @ Sun, 21 Jun 2020 21:17:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.10_model.r WARNING @ Sun, 21 Jun 2020 21:17:44: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:17:44: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Sun, 21 Jun 2020 21:17:44: #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 21:17:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:17:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:17:44: 8000000 INFO @ Sun, 21 Jun 2020 21:17:50: 9000000 INFO @ Sun, 21 Jun 2020 21:17:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:17:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:17:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.05_summits.bed INFO @ Sun, 21 Jun 2020 21:17:54: Done! pass1 - making usageList (1093 chroms): 3 millis pass2 - checking and writing primary data (8629 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:17:55: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:18:01: 11000000 INFO @ Sun, 21 Jun 2020 21:18:06: 12000000 INFO @ Sun, 21 Jun 2020 21:18:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:18:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:18:11: #1 total tags in treatment: 12899936 INFO @ Sun, 21 Jun 2020 21:18:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:18:11: #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 21:18:12: #1 tags after filtering in treatment: 12899884 INFO @ Sun, 21 Jun 2020 21:18:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:18:12: #1 finished! INFO @ Sun, 21 Jun 2020 21:18:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:18:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:18:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:13: #2 number of paired peaks: 6578 INFO @ Sun, 21 Jun 2020 21:18:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:18:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:18:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:18:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:18:13: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 21:18:13: #2 alternative fragment length(s) may be 3,72 bps INFO @ Sun, 21 Jun 2020 21:18:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.20_model.r WARNING @ Sun, 21 Jun 2020 21:18:13: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:18:13: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Sun, 21 Jun 2020 21:18:13: #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 21:18:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:18:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:18:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.10_summits.bed INFO @ Sun, 21 Jun 2020 21:18:27: Done! pass1 - making usageList (970 chroms): 2 millis pass2 - checking and writing primary data (4351 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:18:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923181/SRX4923181.20_summits.bed INFO @ Sun, 21 Jun 2020 21:18:57: Done! pass1 - making usageList (745 chroms): 1 millis pass2 - checking and writing primary data (2300 records, 4 fields): 24 millis CompletedMACS2peakCalling