Job ID = 6453270 SRX = SRX110784 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:13:03 prefetch.2.10.7: 1) Downloading 'SRR388366'... 2020-06-21T08:13:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:19:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:19:49 prefetch.2.10.7: 1) 'SRR388366' was downloaded successfully Read 34319261 spots for SRR388366/SRR388366.sra Written 34319261 spots for SRR388366/SRR388366.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: 00:06:18 34319261 reads; of these: 34319261 (100.00%) were unpaired; of these: 4506808 (13.13%) aligned 0 times 25751098 (75.03%) aligned exactly 1 time 4061355 (11.83%) aligned >1 times 86.87% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 4614668 / 29812453 = 0.1548 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 17:34:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.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 17:34:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:13: 1000000 INFO @ Sun, 21 Jun 2020 17:34:18: 2000000 INFO @ Sun, 21 Jun 2020 17:34:23: 3000000 INFO @ Sun, 21 Jun 2020 17:34:28: 4000000 INFO @ Sun, 21 Jun 2020 17:34:33: 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 17:34:38: 6000000 INFO @ Sun, 21 Jun 2020 17:34:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.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 17:34:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:43: 7000000 INFO @ Sun, 21 Jun 2020 17:34:44: 1000000 INFO @ Sun, 21 Jun 2020 17:34:49: 8000000 INFO @ Sun, 21 Jun 2020 17:34:49: 2000000 INFO @ Sun, 21 Jun 2020 17:34:54: 9000000 INFO @ Sun, 21 Jun 2020 17:34:55: 3000000 INFO @ Sun, 21 Jun 2020 17:34:59: 10000000 INFO @ Sun, 21 Jun 2020 17:35:00: 4000000 INFO @ Sun, 21 Jun 2020 17:35:05: 11000000 INFO @ Sun, 21 Jun 2020 17:35:05: 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 17:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.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 17:35:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:35:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:35:10: 12000000 INFO @ Sun, 21 Jun 2020 17:35:11: 6000000 INFO @ Sun, 21 Jun 2020 17:35:14: 1000000 INFO @ Sun, 21 Jun 2020 17:35:16: 13000000 INFO @ Sun, 21 Jun 2020 17:35:16: 7000000 INFO @ Sun, 21 Jun 2020 17:35:20: 2000000 INFO @ Sun, 21 Jun 2020 17:35:22: 14000000 INFO @ Sun, 21 Jun 2020 17:35:22: 8000000 INFO @ Sun, 21 Jun 2020 17:35:26: 3000000 INFO @ Sun, 21 Jun 2020 17:35:27: 15000000 INFO @ Sun, 21 Jun 2020 17:35:28: 9000000 INFO @ Sun, 21 Jun 2020 17:35:33: 4000000 INFO @ Sun, 21 Jun 2020 17:35:33: 16000000 INFO @ Sun, 21 Jun 2020 17:35:33: 10000000 INFO @ Sun, 21 Jun 2020 17:35:39: 17000000 INFO @ Sun, 21 Jun 2020 17:35:39: 5000000 INFO @ Sun, 21 Jun 2020 17:35:39: 11000000 INFO @ Sun, 21 Jun 2020 17:35:44: 18000000 INFO @ Sun, 21 Jun 2020 17:35:45: 12000000 INFO @ Sun, 21 Jun 2020 17:35:45: 6000000 INFO @ Sun, 21 Jun 2020 17:35:50: 19000000 INFO @ Sun, 21 Jun 2020 17:35:50: 13000000 INFO @ Sun, 21 Jun 2020 17:35:51: 7000000 INFO @ Sun, 21 Jun 2020 17:35:55: 20000000 INFO @ Sun, 21 Jun 2020 17:35:56: 14000000 INFO @ Sun, 21 Jun 2020 17:35:57: 8000000 INFO @ Sun, 21 Jun 2020 17:36:01: 21000000 INFO @ Sun, 21 Jun 2020 17:36:01: 15000000 INFO @ Sun, 21 Jun 2020 17:36:03: 9000000 INFO @ Sun, 21 Jun 2020 17:36:07: 22000000 INFO @ Sun, 21 Jun 2020 17:36:07: 16000000 INFO @ Sun, 21 Jun 2020 17:36:09: 10000000 INFO @ Sun, 21 Jun 2020 17:36:13: 23000000 INFO @ Sun, 21 Jun 2020 17:36:13: 17000000 INFO @ Sun, 21 Jun 2020 17:36:15: 11000000 INFO @ Sun, 21 Jun 2020 17:36:18: 24000000 INFO @ Sun, 21 Jun 2020 17:36:18: 18000000 INFO @ Sun, 21 Jun 2020 17:36:21: 12000000 INFO @ Sun, 21 Jun 2020 17:36:24: 25000000 INFO @ Sun, 21 Jun 2020 17:36:24: 19000000 INFO @ Sun, 21 Jun 2020 17:36:25: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:36:25: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:36:25: #1 total tags in treatment: 25197785 INFO @ Sun, 21 Jun 2020 17:36:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:36:25: #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 17:36:26: #1 tags after filtering in treatment: 25197782 INFO @ Sun, 21 Jun 2020 17:36:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:36:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:36:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:36:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:36:27: #2 number of paired peaks: 304 WARNING @ Sun, 21 Jun 2020 17:36:27: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Sun, 21 Jun 2020 17:36:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:36:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:36:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:36:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:36:28: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 17:36:28: #2 alternative fragment length(s) may be 3,36,51 bps INFO @ Sun, 21 Jun 2020 17:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.05_model.r WARNING @ Sun, 21 Jun 2020 17:36:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:36:28: #2 You may need to consider one of the other alternative d(s): 3,36,51 WARNING @ Sun, 21 Jun 2020 17:36:28: #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 17:36:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:36:28: 13000000 INFO @ Sun, 21 Jun 2020 17:36:29: 20000000 INFO @ Sun, 21 Jun 2020 17:36:34: 14000000 INFO @ Sun, 21 Jun 2020 17:36:35: 21000000 INFO @ Sun, 21 Jun 2020 17:36:40: 15000000 INFO @ Sun, 21 Jun 2020 17:36:41: 22000000 INFO @ Sun, 21 Jun 2020 17:36:46: 16000000 INFO @ Sun, 21 Jun 2020 17:36:46: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:36:52: 24000000 INFO @ Sun, 21 Jun 2020 17:36:52: 17000000 INFO @ Sun, 21 Jun 2020 17:36:57: 25000000 INFO @ Sun, 21 Jun 2020 17:36:58: 18000000 INFO @ Sun, 21 Jun 2020 17:36:59: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:36:59: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:36:59: #1 total tags in treatment: 25197785 INFO @ Sun, 21 Jun 2020 17:36:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:36:59: #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 17:36:59: #1 tags after filtering in treatment: 25197782 INFO @ Sun, 21 Jun 2020 17:36:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:36:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:36:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:36:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:37:01: #2 number of paired peaks: 304 WARNING @ Sun, 21 Jun 2020 17:37:01: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Sun, 21 Jun 2020 17:37:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:01: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 17:37:01: #2 alternative fragment length(s) may be 3,36,51 bps INFO @ Sun, 21 Jun 2020 17:37:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.10_model.r WARNING @ Sun, 21 Jun 2020 17:37:01: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:37:01: #2 You may need to consider one of the other alternative d(s): 3,36,51 WARNING @ Sun, 21 Jun 2020 17:37:01: #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 17:37:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:37:04: 19000000 INFO @ Sun, 21 Jun 2020 17:37:09: 20000000 INFO @ Sun, 21 Jun 2020 17:37:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:37:16: 21000000 INFO @ Sun, 21 Jun 2020 17:37:21: 22000000 INFO @ Sun, 21 Jun 2020 17:37:27: 23000000 INFO @ Sun, 21 Jun 2020 17:37:32: 24000000 INFO @ Sun, 21 Jun 2020 17:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.05_summits.bed INFO @ Sun, 21 Jun 2020 17:37:37: Done! pass1 - making usageList (447 chroms): 3 millis pass2 - checking and writing primary data (15952 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:37:38: 25000000 INFO @ Sun, 21 Jun 2020 17:37:40: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:37:40: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:37:40: #1 total tags in treatment: 25197785 INFO @ Sun, 21 Jun 2020 17:37:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:37:40: #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 17:37:40: #1 tags after filtering in treatment: 25197782 INFO @ Sun, 21 Jun 2020 17:37:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:37:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:37:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:37:40: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:37:42: #2 number of paired peaks: 304 WARNING @ Sun, 21 Jun 2020 17:37:42: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Sun, 21 Jun 2020 17:37:42: start model_add_line... INFO @ Sun, 21 Jun 2020 17:37:42: start X-correlation... INFO @ Sun, 21 Jun 2020 17:37:42: end of X-cor INFO @ Sun, 21 Jun 2020 17:37:42: #2 finished! INFO @ Sun, 21 Jun 2020 17:37:42: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 17:37:42: #2 alternative fragment length(s) may be 3,36,51 bps INFO @ Sun, 21 Jun 2020 17:37:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.20_model.r WARNING @ Sun, 21 Jun 2020 17:37:42: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:37:42: #2 You may need to consider one of the other alternative d(s): 3,36,51 WARNING @ Sun, 21 Jun 2020 17:37:42: #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 17:37:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:37:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:37:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.10_summits.bed INFO @ Sun, 21 Jun 2020 17:38:05: Done! pass1 - making usageList (355 chroms): 2 millis pass2 - checking and writing primary data (7821 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:38:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:38:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:38:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:38:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110784/SRX110784.20_summits.bed INFO @ Sun, 21 Jun 2020 17:38:48: Done! pass1 - making usageList (102 chroms): 1 millis pass2 - checking and writing primary data (1293 records, 4 fields): 5 millis CompletedMACS2peakCalling