Job ID = 6455304 SRX = SRX287678 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:02:41 prefetch.2.10.7: 1) Downloading 'SRR869866'... 2020-06-21T10:02:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:16 prefetch.2.10.7: 1) 'SRR869866' was downloaded successfully Read 18249589 spots for SRR869866/SRR869866.sra Written 18249589 spots for SRR869866/SRR869866.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: 00:04:52 18249589 reads; of these: 18249589 (100.00%) were unpaired; of these: 1102798 (6.04%) aligned 0 times 13105512 (71.81%) aligned exactly 1 time 4041279 (22.14%) aligned >1 times 93.96% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 2105967 / 17146791 = 0.1228 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 19:15:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.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 19:15:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:36: 1000000 INFO @ Sun, 21 Jun 2020 19:15:41: 2000000 INFO @ Sun, 21 Jun 2020 19:15:46: 3000000 INFO @ Sun, 21 Jun 2020 19:15:51: 4000000 INFO @ Sun, 21 Jun 2020 19:15:56: 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 19:16:01: 6000000 INFO @ Sun, 21 Jun 2020 19:16:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.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 19:16:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:06: 7000000 INFO @ Sun, 21 Jun 2020 19:16:07: 1000000 INFO @ Sun, 21 Jun 2020 19:16:11: 8000000 INFO @ Sun, 21 Jun 2020 19:16:12: 2000000 INFO @ Sun, 21 Jun 2020 19:16:16: 9000000 INFO @ Sun, 21 Jun 2020 19:16:17: 3000000 INFO @ Sun, 21 Jun 2020 19:16:21: 10000000 INFO @ Sun, 21 Jun 2020 19:16:22: 4000000 INFO @ Sun, 21 Jun 2020 19:16:27: 11000000 INFO @ Sun, 21 Jun 2020 19:16:27: 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 19:16:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.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 19:16:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:16:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:16:32: 12000000 INFO @ Sun, 21 Jun 2020 19:16:33: 6000000 INFO @ Sun, 21 Jun 2020 19:16:37: 1000000 INFO @ Sun, 21 Jun 2020 19:16:38: 13000000 INFO @ Sun, 21 Jun 2020 19:16:38: 7000000 INFO @ Sun, 21 Jun 2020 19:16:42: 2000000 INFO @ Sun, 21 Jun 2020 19:16:43: 14000000 INFO @ Sun, 21 Jun 2020 19:16:43: 8000000 INFO @ Sun, 21 Jun 2020 19:16:47: 3000000 INFO @ Sun, 21 Jun 2020 19:16:48: 15000000 INFO @ Sun, 21 Jun 2020 19:16:48: 9000000 INFO @ Sun, 21 Jun 2020 19:16:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:49: #1 total tags in treatment: 15040824 INFO @ Sun, 21 Jun 2020 19:16:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:49: #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 19:16:49: #1 tags after filtering in treatment: 15040823 INFO @ Sun, 21 Jun 2020 19:16:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:50: #2 number of paired peaks: 316 WARNING @ Sun, 21 Jun 2020 19:16:50: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:50: #2 predicted fragment length is 31 bps INFO @ Sun, 21 Jun 2020 19:16:50: #2 alternative fragment length(s) may be 3,31 bps INFO @ Sun, 21 Jun 2020 19:16:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.05_model.r WARNING @ Sun, 21 Jun 2020 19:16:50: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:16:50: #2 You may need to consider one of the other alternative d(s): 3,31 WARNING @ Sun, 21 Jun 2020 19:16:50: #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 19:16:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:52: 4000000 INFO @ Sun, 21 Jun 2020 19:16:53: 10000000 INFO @ Sun, 21 Jun 2020 19:16:57: 5000000 INFO @ Sun, 21 Jun 2020 19:16:59: 11000000 INFO @ Sun, 21 Jun 2020 19:17:03: 6000000 INFO @ Sun, 21 Jun 2020 19:17:04: 12000000 INFO @ Sun, 21 Jun 2020 19:17:08: 7000000 INFO @ Sun, 21 Jun 2020 19:17:09: 13000000 INFO @ Sun, 21 Jun 2020 19:17:13: 8000000 INFO @ Sun, 21 Jun 2020 19:17:15: 14000000 INFO @ Sun, 21 Jun 2020 19:17:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:18: 9000000 INFO @ Sun, 21 Jun 2020 19:17:20: 15000000 INFO @ Sun, 21 Jun 2020 19:17:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:20: #1 total tags in treatment: 15040824 INFO @ Sun, 21 Jun 2020 19:17:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:20: #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 19:17:21: #1 tags after filtering in treatment: 15040823 INFO @ Sun, 21 Jun 2020 19:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:22: #2 number of paired peaks: 316 WARNING @ Sun, 21 Jun 2020 19:17:22: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:22: #2 predicted fragment length is 31 bps INFO @ Sun, 21 Jun 2020 19:17:22: #2 alternative fragment length(s) may be 3,31 bps INFO @ Sun, 21 Jun 2020 19:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.10_model.r WARNING @ Sun, 21 Jun 2020 19:17:22: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:17:22: #2 You may need to consider one of the other alternative d(s): 3,31 WARNING @ Sun, 21 Jun 2020 19:17:22: #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 19:17:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:23: 10000000 INFO @ Sun, 21 Jun 2020 19:17:28: 11000000 INFO @ Sun, 21 Jun 2020 19:17:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.05_summits.bed INFO @ Sun, 21 Jun 2020 19:17:30: Done! pass1 - making usageList (492 chroms): 1 millis pass2 - checking and writing primary data (2165 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:17:33: 12000000 INFO @ Sun, 21 Jun 2020 19:17:39: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:17:44: 14000000 INFO @ Sun, 21 Jun 2020 19:17:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:49: 15000000 INFO @ Sun, 21 Jun 2020 19:17:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:49: #1 total tags in treatment: 15040824 INFO @ Sun, 21 Jun 2020 19:17:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:49: #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 19:17:50: #1 tags after filtering in treatment: 15040823 INFO @ Sun, 21 Jun 2020 19:17:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:51: #2 number of paired peaks: 316 WARNING @ Sun, 21 Jun 2020 19:17:51: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:51: #2 predicted fragment length is 31 bps INFO @ Sun, 21 Jun 2020 19:17:51: #2 alternative fragment length(s) may be 3,31 bps INFO @ Sun, 21 Jun 2020 19:17:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.20_model.r WARNING @ Sun, 21 Jun 2020 19:17:51: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:17:51: #2 You may need to consider one of the other alternative d(s): 3,31 WARNING @ Sun, 21 Jun 2020 19:17:51: #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 19:17:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.10_summits.bed INFO @ Sun, 21 Jun 2020 19:18:02: Done! pass1 - making usageList (369 chroms): 1 millis pass2 - checking and writing primary data (1039 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:18:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287678/SRX287678.20_summits.bed INFO @ Sun, 21 Jun 2020 19:18:31: Done! pass1 - making usageList (175 chroms): 1 millis pass2 - checking and writing primary data (377 records, 4 fields): 7 millis CompletedMACS2peakCalling