Job ID = 6456225 SRX = SRX331381 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:44:23 prefetch.2.10.7: 1) Downloading 'SRR947618'... 2020-06-21T10:44:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:47:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:47:48 prefetch.2.10.7: 1) 'SRR947618' was downloaded successfully Read 18493128 spots for SRR947618/SRR947618.sra Written 18493128 spots for SRR947618/SRR947618.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: 00:04:55 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1284034 (6.94%) aligned 0 times 13226986 (71.52%) aligned exactly 1 time 3982108 (21.53%) aligned >1 times 93.06% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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] 1869123 / 17209094 = 0.1086 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 19:58:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.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 19:58:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:16: 1000000 INFO @ Sun, 21 Jun 2020 19:58:22: 2000000 INFO @ Sun, 21 Jun 2020 19:58:29: 3000000 INFO @ Sun, 21 Jun 2020 19:58:35: 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 19:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.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 19:58:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:41: 5000000 INFO @ Sun, 21 Jun 2020 19:58:46: 1000000 INFO @ Sun, 21 Jun 2020 19:58:48: 6000000 INFO @ Sun, 21 Jun 2020 19:58:51: 2000000 INFO @ Sun, 21 Jun 2020 19:58:55: 7000000 INFO @ Sun, 21 Jun 2020 19:58:57: 3000000 INFO @ Sun, 21 Jun 2020 19:59:01: 8000000 INFO @ Sun, 21 Jun 2020 19:59:03: 4000000 INFO @ Sun, 21 Jun 2020 19:59:08: 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 19:59:09: 5000000 INFO @ Sun, 21 Jun 2020 19:59:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.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 19:59:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:59:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:59:14: 10000000 INFO @ Sun, 21 Jun 2020 19:59:15: 6000000 INFO @ Sun, 21 Jun 2020 19:59:16: 1000000 INFO @ Sun, 21 Jun 2020 19:59:21: 7000000 INFO @ Sun, 21 Jun 2020 19:59:21: 11000000 INFO @ Sun, 21 Jun 2020 19:59:22: 2000000 INFO @ Sun, 21 Jun 2020 19:59:27: 8000000 INFO @ Sun, 21 Jun 2020 19:59:27: 12000000 INFO @ Sun, 21 Jun 2020 19:59:28: 3000000 INFO @ Sun, 21 Jun 2020 19:59:33: 9000000 INFO @ Sun, 21 Jun 2020 19:59:34: 4000000 INFO @ Sun, 21 Jun 2020 19:59:34: 13000000 INFO @ Sun, 21 Jun 2020 19:59:38: 10000000 INFO @ Sun, 21 Jun 2020 19:59:40: 5000000 INFO @ Sun, 21 Jun 2020 19:59:41: 14000000 INFO @ Sun, 21 Jun 2020 19:59:44: 11000000 INFO @ Sun, 21 Jun 2020 19:59:46: 6000000 INFO @ Sun, 21 Jun 2020 19:59:47: 15000000 INFO @ Sun, 21 Jun 2020 19:59:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:59:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:59:50: #1 total tags in treatment: 15339971 INFO @ Sun, 21 Jun 2020 19:59:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:50: #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 19:59:50: #1 tags after filtering in treatment: 15339970 INFO @ Sun, 21 Jun 2020 19:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:50: 12000000 INFO @ Sun, 21 Jun 2020 19:59:51: #2 number of paired peaks: 309 WARNING @ Sun, 21 Jun 2020 19:59:51: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 21 Jun 2020 19:59:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:51: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:59:51: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.05_model.r WARNING @ Sun, 21 Jun 2020 19:59:51: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:59:51: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:59:51: #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 19:59:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:52: 7000000 INFO @ Sun, 21 Jun 2020 19:59:56: 13000000 INFO @ Sun, 21 Jun 2020 19:59:58: 8000000 INFO @ Sun, 21 Jun 2020 20:00:02: 14000000 INFO @ Sun, 21 Jun 2020 20:00:03: 9000000 INFO @ Sun, 21 Jun 2020 20:00:08: 15000000 INFO @ Sun, 21 Jun 2020 20:00:09: 10000000 INFO @ Sun, 21 Jun 2020 20:00:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:00:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:00:10: #1 total tags in treatment: 15339971 INFO @ Sun, 21 Jun 2020 20:00:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:10: #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 20:00:11: #1 tags after filtering in treatment: 15339970 INFO @ Sun, 21 Jun 2020 20:00:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:11: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:12: #2 number of paired peaks: 309 WARNING @ Sun, 21 Jun 2020 20:00:12: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:12: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:12: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:12: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:12: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:12: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 20:00:12: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 20:00:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.10_model.r WARNING @ Sun, 21 Jun 2020 20:00:12: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:00:12: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 20:00:12: #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 20:00:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:15: 11000000 INFO @ Sun, 21 Jun 2020 20:00:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:20: 12000000 INFO @ Sun, 21 Jun 2020 20:00:26: 13000000 INFO @ Sun, 21 Jun 2020 20:00:31: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.05_summits.bed INFO @ Sun, 21 Jun 2020 20:00:34: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (2092 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:00:37: 15000000 INFO @ Sun, 21 Jun 2020 20:00:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:00:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:00:39: #1 total tags in treatment: 15339971 INFO @ Sun, 21 Jun 2020 20:00:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:39: #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 20:00:40: #1 tags after filtering in treatment: 15339970 INFO @ Sun, 21 Jun 2020 20:00:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:41: #2 number of paired peaks: 309 WARNING @ Sun, 21 Jun 2020 20:00:41: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:41: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 20:00:41: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 20:00:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.20_model.r WARNING @ Sun, 21 Jun 2020 20:00:41: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:00:41: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 20:00:41: #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 20:00:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.10_summits.bed INFO @ Sun, 21 Jun 2020 20:00:56: Done! pass1 - making usageList (430 chroms): 1 millis pass2 - checking and writing primary data (1358 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:01:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331381/SRX331381.20_summits.bed INFO @ Sun, 21 Jun 2020 20:01:24: Done! pass1 - making usageList (208 chroms): 0 millis pass2 - checking and writing primary data (465 records, 4 fields): 8 millis CompletedMACS2peakCalling