Job ID = 6458465 SRX = SRX5241029 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:38:43 prefetch.2.10.7: 1) Downloading 'SRR8433310'... 2020-06-21T12:38:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:41:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:41:25 prefetch.2.10.7: 1) 'SRR8433310' was downloaded successfully 2020-06-21T12:41:25 prefetch.2.10.7: 'SRR8433310' has 0 unresolved dependencies Read 21616990 spots for SRR8433310/SRR8433310.sra Written 21616990 spots for SRR8433310/SRR8433310.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: 00:07:38 21616990 reads; of these: 21616990 (100.00%) were unpaired; of these: 1091001 (5.05%) aligned 0 times 16705936 (77.28%) aligned exactly 1 time 3820053 (17.67%) aligned >1 times 94.95% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 2157547 / 20525989 = 0.1051 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 21:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.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 21:56:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:10: 1000000 INFO @ Sun, 21 Jun 2020 21:56:16: 2000000 INFO @ Sun, 21 Jun 2020 21:56:23: 3000000 INFO @ Sun, 21 Jun 2020 21:56:29: 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 21:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.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 21:56:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:36: 5000000 INFO @ Sun, 21 Jun 2020 21:56:41: 1000000 INFO @ Sun, 21 Jun 2020 21:56:43: 6000000 INFO @ Sun, 21 Jun 2020 21:56:48: 2000000 INFO @ Sun, 21 Jun 2020 21:56:51: 7000000 INFO @ Sun, 21 Jun 2020 21:56:56: 3000000 INFO @ Sun, 21 Jun 2020 21:56:58: 8000000 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 21:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.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 21:57:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:04: 4000000 INFO @ Sun, 21 Jun 2020 21:57:06: 9000000 INFO @ Sun, 21 Jun 2020 21:57:12: 1000000 INFO @ Sun, 21 Jun 2020 21:57:12: 5000000 INFO @ Sun, 21 Jun 2020 21:57:14: 10000000 INFO @ Sun, 21 Jun 2020 21:57:20: 2000000 INFO @ Sun, 21 Jun 2020 21:57:20: 6000000 INFO @ Sun, 21 Jun 2020 21:57:22: 11000000 INFO @ Sun, 21 Jun 2020 21:57:28: 7000000 INFO @ Sun, 21 Jun 2020 21:57:28: 3000000 INFO @ Sun, 21 Jun 2020 21:57:30: 12000000 INFO @ Sun, 21 Jun 2020 21:57:36: 8000000 INFO @ Sun, 21 Jun 2020 21:57:36: 4000000 INFO @ Sun, 21 Jun 2020 21:57:37: 13000000 INFO @ Sun, 21 Jun 2020 21:57:44: 5000000 INFO @ Sun, 21 Jun 2020 21:57:44: 9000000 INFO @ Sun, 21 Jun 2020 21:57:45: 14000000 INFO @ Sun, 21 Jun 2020 21:57:52: 6000000 INFO @ Sun, 21 Jun 2020 21:57:52: 10000000 INFO @ Sun, 21 Jun 2020 21:57:53: 15000000 INFO @ Sun, 21 Jun 2020 21:57:59: 7000000 INFO @ Sun, 21 Jun 2020 21:58:00: 11000000 INFO @ Sun, 21 Jun 2020 21:58:01: 16000000 INFO @ Sun, 21 Jun 2020 21:58:07: 8000000 INFO @ Sun, 21 Jun 2020 21:58:08: 12000000 INFO @ Sun, 21 Jun 2020 21:58:09: 17000000 INFO @ Sun, 21 Jun 2020 21:58:15: 13000000 INFO @ Sun, 21 Jun 2020 21:58:15: 9000000 INFO @ Sun, 21 Jun 2020 21:58:17: 18000000 INFO @ Sun, 21 Jun 2020 21:58:20: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:58:20: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:58:20: #1 total tags in treatment: 18368442 INFO @ Sun, 21 Jun 2020 21:58:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:20: #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 21:58:20: #1 tags after filtering in treatment: 18368318 INFO @ Sun, 21 Jun 2020 21:58:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:22: #2 number of paired peaks: 198 WARNING @ Sun, 21 Jun 2020 21:58:22: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Sun, 21 Jun 2020 21:58:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:22: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:58:22: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sun, 21 Jun 2020 21:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.05_model.r WARNING @ Sun, 21 Jun 2020 21:58:22: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:22: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Sun, 21 Jun 2020 21:58:22: #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 21:58:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:23: 14000000 INFO @ Sun, 21 Jun 2020 21:58:23: 10000000 INFO @ Sun, 21 Jun 2020 21:58:31: 11000000 INFO @ Sun, 21 Jun 2020 21:58:31: 15000000 INFO @ Sun, 21 Jun 2020 21:58:38: 12000000 INFO @ Sun, 21 Jun 2020 21:58:39: 16000000 INFO @ Sun, 21 Jun 2020 21:58:45: 13000000 INFO @ Sun, 21 Jun 2020 21:58:47: 17000000 INFO @ Sun, 21 Jun 2020 21:58:52: 14000000 INFO @ Sun, 21 Jun 2020 21:58:54: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:58:57: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:58:57: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:58:57: #1 total tags in treatment: 18368442 INFO @ Sun, 21 Jun 2020 21:58:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:57: #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 21:58:58: #1 tags after filtering in treatment: 18368318 INFO @ Sun, 21 Jun 2020 21:58:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:59: #2 number of paired peaks: 198 WARNING @ Sun, 21 Jun 2020 21:58:59: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Sun, 21 Jun 2020 21:58:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:59: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:58:59: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sun, 21 Jun 2020 21:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.10_model.r WARNING @ Sun, 21 Jun 2020 21:58:59: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:59: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Sun, 21 Jun 2020 21:58:59: #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 21:58:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:00: 15000000 INFO @ Sun, 21 Jun 2020 21:59:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:07: 16000000 INFO @ Sun, 21 Jun 2020 21:59:14: 17000000 INFO @ Sun, 21 Jun 2020 21:59:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.05_summits.bed INFO @ Sun, 21 Jun 2020 21:59:20: Done! INFO @ Sun, 21 Jun 2020 21:59:20: 18000000 pass1 - making usageList (423 chroms): 1 millis pass2 - checking and writing primary data (3286 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:23: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:59:23: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:59:23: #1 total tags in treatment: 18368442 INFO @ Sun, 21 Jun 2020 21:59:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:23: #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 21:59:24: #1 tags after filtering in treatment: 18368318 INFO @ Sun, 21 Jun 2020 21:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:25: #2 number of paired peaks: 198 WARNING @ Sun, 21 Jun 2020 21:59:25: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:25: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:59:25: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sun, 21 Jun 2020 21:59:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.20_model.r WARNING @ Sun, 21 Jun 2020 21:59:25: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:25: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Sun, 21 Jun 2020 21:59:25: #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 21:59:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:59:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.10_summits.bed INFO @ Sun, 21 Jun 2020 21:59:57: Done! pass1 - making usageList (241 chroms): 1 millis pass2 - checking and writing primary data (841 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5241029/SRX5241029.20_summits.bed INFO @ Sun, 21 Jun 2020 22:00:22: Done! pass1 - making usageList (118 chroms): 0 millis pass2 - checking and writing primary data (268 records, 4 fields): 6 millis CompletedMACS2peakCalling