Job ID = 6456445 SRX = SRX3404042 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:50:46 prefetch.2.10.7: 1) Downloading 'SRR6303519'... 2020-06-21T10:50:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:54:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:54:20 prefetch.2.10.7: 'SRR6303519' is valid 2020-06-21T10:54:20 prefetch.2.10.7: 1) 'SRR6303519' was downloaded successfully 2020-06-21T10:54:20 prefetch.2.10.7: 'SRR6303519' has 0 unresolved dependencies Read 21356281 spots for SRR6303519/SRR6303519.sra Written 21356281 spots for SRR6303519/SRR6303519.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:03 21356281 reads; of these: 21356281 (100.00%) were unpaired; of these: 750917 (3.52%) aligned 0 times 14774674 (69.18%) aligned exactly 1 time 5830690 (27.30%) aligned >1 times 96.48% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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] 2215488 / 20605364 = 0.1075 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 20:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.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 20:06:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:25: 1000000 INFO @ Sun, 21 Jun 2020 20:06:32: 2000000 INFO @ Sun, 21 Jun 2020 20:06:39: 3000000 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 20:06:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.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 20:06:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:46: 4000000 INFO @ Sun, 21 Jun 2020 20:06:52: 1000000 INFO @ Sun, 21 Jun 2020 20:06:54: 5000000 INFO @ Sun, 21 Jun 2020 20:06:58: 2000000 INFO @ Sun, 21 Jun 2020 20:07:02: 6000000 INFO @ Sun, 21 Jun 2020 20:07:05: 3000000 INFO @ Sun, 21 Jun 2020 20:07:10: 7000000 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 20:07:12: 4000000 INFO @ Sun, 21 Jun 2020 20:07:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.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 20:07:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:17: 8000000 INFO @ Sun, 21 Jun 2020 20:07:20: 5000000 INFO @ Sun, 21 Jun 2020 20:07:21: 1000000 INFO @ Sun, 21 Jun 2020 20:07:25: 9000000 INFO @ Sun, 21 Jun 2020 20:07:27: 6000000 INFO @ Sun, 21 Jun 2020 20:07:29: 2000000 INFO @ Sun, 21 Jun 2020 20:07:33: 10000000 INFO @ Sun, 21 Jun 2020 20:07:34: 7000000 INFO @ Sun, 21 Jun 2020 20:07:36: 3000000 INFO @ Sun, 21 Jun 2020 20:07:41: 11000000 INFO @ Sun, 21 Jun 2020 20:07:42: 8000000 INFO @ Sun, 21 Jun 2020 20:07:44: 4000000 INFO @ Sun, 21 Jun 2020 20:07:49: 12000000 INFO @ Sun, 21 Jun 2020 20:07:49: 9000000 INFO @ Sun, 21 Jun 2020 20:07:51: 5000000 INFO @ Sun, 21 Jun 2020 20:07:56: 10000000 INFO @ Sun, 21 Jun 2020 20:07:57: 13000000 INFO @ Sun, 21 Jun 2020 20:07:58: 6000000 INFO @ Sun, 21 Jun 2020 20:08:04: 11000000 INFO @ Sun, 21 Jun 2020 20:08:05: 14000000 INFO @ Sun, 21 Jun 2020 20:08:06: 7000000 INFO @ Sun, 21 Jun 2020 20:08:11: 12000000 INFO @ Sun, 21 Jun 2020 20:08:12: 15000000 INFO @ Sun, 21 Jun 2020 20:08:13: 8000000 INFO @ Sun, 21 Jun 2020 20:08:18: 13000000 INFO @ Sun, 21 Jun 2020 20:08:20: 9000000 INFO @ Sun, 21 Jun 2020 20:08:21: 16000000 INFO @ Sun, 21 Jun 2020 20:08:26: 14000000 INFO @ Sun, 21 Jun 2020 20:08:28: 10000000 INFO @ Sun, 21 Jun 2020 20:08:28: 17000000 INFO @ Sun, 21 Jun 2020 20:08:33: 15000000 INFO @ Sun, 21 Jun 2020 20:08:35: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:08:36: 18000000 INFO @ Sun, 21 Jun 2020 20:08:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:08:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:08:39: #1 total tags in treatment: 18389876 INFO @ Sun, 21 Jun 2020 20:08:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:39: #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 20:08:40: #1 tags after filtering in treatment: 18389809 INFO @ Sun, 21 Jun 2020 20:08:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:40: 16000000 INFO @ Sun, 21 Jun 2020 20:08:41: #2 number of paired peaks: 873 WARNING @ Sun, 21 Jun 2020 20:08:41: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Sun, 21 Jun 2020 20:08:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:41: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 20:08:41: #2 alternative fragment length(s) may be 3,78 bps INFO @ Sun, 21 Jun 2020 20:08:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.05_model.r WARNING @ Sun, 21 Jun 2020 20:08:41: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:41: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Sun, 21 Jun 2020 20:08:41: #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 20:08:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:42: 12000000 INFO @ Sun, 21 Jun 2020 20:08:47: 17000000 INFO @ Sun, 21 Jun 2020 20:08:48: 13000000 INFO @ Sun, 21 Jun 2020 20:08:53: 18000000 INFO @ Sun, 21 Jun 2020 20:08:55: 14000000 INFO @ Sun, 21 Jun 2020 20:08:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:08:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:08:56: #1 total tags in treatment: 18389876 INFO @ Sun, 21 Jun 2020 20:08:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:56: #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 20:08:57: #1 tags after filtering in treatment: 18389809 INFO @ Sun, 21 Jun 2020 20:08:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:57: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:58: #2 number of paired peaks: 873 WARNING @ Sun, 21 Jun 2020 20:08:58: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Sun, 21 Jun 2020 20:08:58: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:58: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:58: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:58: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:58: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 20:08:58: #2 alternative fragment length(s) may be 3,78 bps INFO @ Sun, 21 Jun 2020 20:08:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.10_model.r WARNING @ Sun, 21 Jun 2020 20:08:58: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:58: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Sun, 21 Jun 2020 20:08:58: #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 20:08:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:01: 15000000 INFO @ Sun, 21 Jun 2020 20:09:08: 16000000 INFO @ Sun, 21 Jun 2020 20:09:13: 17000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:09:19: 18000000 INFO @ Sun, 21 Jun 2020 20:09:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:22: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:09:22: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:09:22: #1 total tags in treatment: 18389876 INFO @ Sun, 21 Jun 2020 20:09:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:22: #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 20:09:22: #1 tags after filtering in treatment: 18389809 INFO @ Sun, 21 Jun 2020 20:09:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:23: #2 number of paired peaks: 873 WARNING @ Sun, 21 Jun 2020 20:09:23: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Sun, 21 Jun 2020 20:09:23: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:24: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:24: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:24: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:24: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 20:09:24: #2 alternative fragment length(s) may be 3,78 bps INFO @ Sun, 21 Jun 2020 20:09:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.20_model.r WARNING @ Sun, 21 Jun 2020 20:09:24: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:09:24: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Sun, 21 Jun 2020 20:09:24: #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 20:09:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.05_summits.bed INFO @ Sun, 21 Jun 2020 20:09:38: Done! pass1 - making usageList (681 chroms): 2 millis pass2 - checking and writing primary data (4001 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.10_summits.bed INFO @ Sun, 21 Jun 2020 20:09:53: Done! pass1 - making usageList (512 chroms): 2 millis pass2 - checking and writing primary data (2234 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:10:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404042/SRX3404042.20_summits.bed INFO @ Sun, 21 Jun 2020 20:10:19: Done! pass1 - making usageList (269 chroms): 1 millis pass2 - checking and writing primary data (989 records, 4 fields): 9 millis CompletedMACS2peakCalling