Job ID = 6454619 SRX = SRX2399661 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:15:54 prefetch.2.10.7: 1) Downloading 'SRR5081495'... 2020-06-21T09:15:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:18:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:18:01 prefetch.2.10.7: 'SRR5081495' is valid 2020-06-21T09:18:01 prefetch.2.10.7: 1) 'SRR5081495' was downloaded successfully 2020-06-21T09:18:01 prefetch.2.10.7: 'SRR5081495' has 0 unresolved dependencies Read 14158373 spots for SRR5081495/SRR5081495.sra Written 14158373 spots for SRR5081495/SRR5081495.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:40 14158373 reads; of these: 14158373 (100.00%) were unpaired; of these: 908506 (6.42%) aligned 0 times 9619416 (67.94%) aligned exactly 1 time 3630451 (25.64%) aligned >1 times 93.58% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 1266211 / 13249867 = 0.0956 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 18:26:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.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 18:26:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:58: 1000000 INFO @ Sun, 21 Jun 2020 18:27:03: 2000000 INFO @ Sun, 21 Jun 2020 18:27:08: 3000000 INFO @ Sun, 21 Jun 2020 18:27:13: 4000000 INFO @ Sun, 21 Jun 2020 18:27:19: 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 18:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.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 18:27:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:24: 6000000 INFO @ Sun, 21 Jun 2020 18:27:27: 1000000 INFO @ Sun, 21 Jun 2020 18:27:29: 7000000 INFO @ Sun, 21 Jun 2020 18:27:33: 2000000 INFO @ Sun, 21 Jun 2020 18:27:34: 8000000 INFO @ Sun, 21 Jun 2020 18:27:38: 3000000 INFO @ Sun, 21 Jun 2020 18:27:40: 9000000 INFO @ Sun, 21 Jun 2020 18:27:43: 4000000 INFO @ Sun, 21 Jun 2020 18:27:45: 10000000 INFO @ Sun, 21 Jun 2020 18:27:49: 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 18:27:51: 11000000 INFO @ Sun, 21 Jun 2020 18:27:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.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 18:27:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:54: 6000000 INFO @ Sun, 21 Jun 2020 18:27:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:27:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:27:56: #1 total tags in treatment: 11983656 INFO @ Sun, 21 Jun 2020 18:27:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:56: #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 18:27:57: #1 tags after filtering in treatment: 11983656 INFO @ Sun, 21 Jun 2020 18:27:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:58: #2 number of paired peaks: 465 WARNING @ Sun, 21 Jun 2020 18:27:58: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Sun, 21 Jun 2020 18:27:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:58: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:27:58: #2 alternative fragment length(s) may be 4,52,589,595 bps INFO @ Sun, 21 Jun 2020 18:27:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.05_model.r WARNING @ Sun, 21 Jun 2020 18:27:58: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:27:58: #2 You may need to consider one of the other alternative d(s): 4,52,589,595 WARNING @ Sun, 21 Jun 2020 18:27:58: #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 18:27:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:58: 1000000 INFO @ Sun, 21 Jun 2020 18:28:00: 7000000 INFO @ Sun, 21 Jun 2020 18:28:04: 2000000 INFO @ Sun, 21 Jun 2020 18:28:05: 8000000 INFO @ Sun, 21 Jun 2020 18:28:10: 3000000 INFO @ Sun, 21 Jun 2020 18:28:11: 9000000 INFO @ Sun, 21 Jun 2020 18:28:15: 4000000 INFO @ Sun, 21 Jun 2020 18:28:17: 10000000 INFO @ Sun, 21 Jun 2020 18:28:21: 5000000 INFO @ Sun, 21 Jun 2020 18:28:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:22: 11000000 INFO @ Sun, 21 Jun 2020 18:28:26: 6000000 INFO @ Sun, 21 Jun 2020 18:28:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:28:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:28:28: #1 total tags in treatment: 11983656 INFO @ Sun, 21 Jun 2020 18:28:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:28: #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 18:28:29: #1 tags after filtering in treatment: 11983656 INFO @ Sun, 21 Jun 2020 18:28:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:29: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:29: #2 number of paired peaks: 465 WARNING @ Sun, 21 Jun 2020 18:28:29: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Sun, 21 Jun 2020 18:28:29: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:30: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:30: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:30: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:30: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:28:30: #2 alternative fragment length(s) may be 4,52,589,595 bps INFO @ Sun, 21 Jun 2020 18:28:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.10_model.r WARNING @ Sun, 21 Jun 2020 18:28:30: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:28:30: #2 You may need to consider one of the other alternative d(s): 4,52,589,595 WARNING @ Sun, 21 Jun 2020 18:28:30: #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 18:28:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:28:32: 7000000 INFO @ Sun, 21 Jun 2020 18:28:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.05_summits.bed INFO @ Sun, 21 Jun 2020 18:28:33: Done! pass1 - making usageList (607 chroms): 2 millis pass2 - checking and writing primary data (2332 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:37: 8000000 INFO @ Sun, 21 Jun 2020 18:28:43: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:28:48: 10000000 INFO @ Sun, 21 Jun 2020 18:28:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:54: 11000000 INFO @ Sun, 21 Jun 2020 18:28:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:28:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:28:59: #1 total tags in treatment: 11983656 INFO @ Sun, 21 Jun 2020 18:28:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:59: #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 18:29:00: #1 tags after filtering in treatment: 11983656 INFO @ Sun, 21 Jun 2020 18:29:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:29:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:29:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:29:01: #2 number of paired peaks: 465 WARNING @ Sun, 21 Jun 2020 18:29:01: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Sun, 21 Jun 2020 18:29:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:29:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:29:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:29:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:29:01: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 18:29:01: #2 alternative fragment length(s) may be 4,52,589,595 bps INFO @ Sun, 21 Jun 2020 18:29:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.20_model.r WARNING @ Sun, 21 Jun 2020 18:29:01: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:29:01: #2 You may need to consider one of the other alternative d(s): 4,52,589,595 WARNING @ Sun, 21 Jun 2020 18:29:01: #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 18:29:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:29:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.10_summits.bed INFO @ Sun, 21 Jun 2020 18:29:05: Done! pass1 - making usageList (449 chroms): 1 millis pass2 - checking and writing primary data (1301 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:29:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399661/SRX2399661.20_summits.bed INFO @ Sun, 21 Jun 2020 18:29:36: Done! pass1 - making usageList (204 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 10 millis CompletedMACS2peakCalling