Job ID = 6456912 SRX = SRX4053338 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:13:54 prefetch.2.10.7: 1) Downloading 'SRR7132375'... 2020-06-21T11:13:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:52 prefetch.2.10.7: 'SRR7132375' is valid 2020-06-21T11:15:52 prefetch.2.10.7: 1) 'SRR7132375' was downloaded successfully 2020-06-21T11:15:52 prefetch.2.10.7: 'SRR7132375' has 0 unresolved dependencies Read 18474302 spots for SRR7132375/SRR7132375.sra Written 18474302 spots for SRR7132375/SRR7132375.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: 00:05:01 18474302 reads; of these: 18474302 (100.00%) were unpaired; of these: 3840168 (20.79%) aligned 0 times 10545765 (57.08%) aligned exactly 1 time 4088369 (22.13%) aligned >1 times 79.21% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 2748781 / 14634134 = 0.1878 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 20:25:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.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 20:25:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:48: 1000000 INFO @ Sun, 21 Jun 2020 20:25:54: 2000000 INFO @ Sun, 21 Jun 2020 20:26:01: 3000000 INFO @ Sun, 21 Jun 2020 20:26:07: 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 20:26:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.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 20:26:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:13: 5000000 INFO @ Sun, 21 Jun 2020 20:26:17: 1000000 INFO @ Sun, 21 Jun 2020 20:26:19: 6000000 INFO @ Sun, 21 Jun 2020 20:26:22: 2000000 INFO @ Sun, 21 Jun 2020 20:26:26: 7000000 INFO @ Sun, 21 Jun 2020 20:26:28: 3000000 INFO @ Sun, 21 Jun 2020 20:26:32: 8000000 INFO @ Sun, 21 Jun 2020 20:26:33: 4000000 INFO @ Sun, 21 Jun 2020 20:26:38: 5000000 INFO @ Sun, 21 Jun 2020 20:26:38: 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 20:26:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.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 20:26:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:43: 6000000 INFO @ Sun, 21 Jun 2020 20:26:45: 10000000 INFO @ Sun, 21 Jun 2020 20:26:48: 1000000 INFO @ Sun, 21 Jun 2020 20:26:49: 7000000 INFO @ Sun, 21 Jun 2020 20:26:51: 11000000 INFO @ Sun, 21 Jun 2020 20:26:54: 2000000 INFO @ Sun, 21 Jun 2020 20:26:54: 8000000 INFO @ Sun, 21 Jun 2020 20:26:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:26:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:26:58: #1 total tags in treatment: 11885353 INFO @ Sun, 21 Jun 2020 20:26:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:58: #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 20:26:58: #1 tags after filtering in treatment: 11885350 INFO @ Sun, 21 Jun 2020 20:26:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:59: #2 number of paired peaks: 227 WARNING @ Sun, 21 Jun 2020 20:26:59: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sun, 21 Jun 2020 20:26:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:59: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 20:26:59: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 21 Jun 2020 20:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.05_model.r WARNING @ Sun, 21 Jun 2020 20:26:59: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:26:59: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 21 Jun 2020 20:26:59: #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 20:26:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:00: 9000000 INFO @ Sun, 21 Jun 2020 20:27:00: 3000000 INFO @ Sun, 21 Jun 2020 20:27:06: 10000000 INFO @ Sun, 21 Jun 2020 20:27:07: 4000000 INFO @ Sun, 21 Jun 2020 20:27:11: 11000000 INFO @ Sun, 21 Jun 2020 20:27:13: 5000000 INFO @ Sun, 21 Jun 2020 20:27:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:27:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:27:17: #1 total tags in treatment: 11885353 INFO @ Sun, 21 Jun 2020 20:27:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:17: #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 20:27:17: #1 tags after filtering in treatment: 11885350 INFO @ Sun, 21 Jun 2020 20:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:18: #2 number of paired peaks: 227 WARNING @ Sun, 21 Jun 2020 20:27:18: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sun, 21 Jun 2020 20:27:18: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:18: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:18: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:18: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:18: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 20:27:18: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 21 Jun 2020 20:27:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.10_model.r WARNING @ Sun, 21 Jun 2020 20:27:18: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:27:18: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 21 Jun 2020 20:27:18: #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 20:27:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:19: 6000000 INFO @ Sun, 21 Jun 2020 20:27:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:25: 7000000 INFO @ Sun, 21 Jun 2020 20:27:31: 8000000 INFO @ Sun, 21 Jun 2020 20:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.05_summits.bed INFO @ Sun, 21 Jun 2020 20:27:35: Done! pass1 - making usageList (635 chroms): 2 millis pass2 - checking and writing primary data (2368 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:27:37: 9000000 INFO @ Sun, 21 Jun 2020 20:27:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:44: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:27:50: 11000000 INFO @ Sun, 21 Jun 2020 20:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.10_summits.bed INFO @ Sun, 21 Jun 2020 20:27:52: Done! pass1 - making usageList (444 chroms): 1 millis pass2 - checking and writing primary data (1032 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:27:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:27:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:27:56: #1 total tags in treatment: 11885353 INFO @ Sun, 21 Jun 2020 20:27:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:56: #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 20:27:57: #1 tags after filtering in treatment: 11885350 INFO @ Sun, 21 Jun 2020 20:27:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:57: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:58: #2 number of paired peaks: 227 WARNING @ Sun, 21 Jun 2020 20:27:58: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sun, 21 Jun 2020 20:27:58: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:58: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:58: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:58: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:58: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 20:27:58: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 21 Jun 2020 20:27:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.20_model.r WARNING @ Sun, 21 Jun 2020 20:27:58: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:27:58: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 21 Jun 2020 20:27:58: #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 20:27:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:28:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:28:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:28:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053338/SRX4053338.20_summits.bed INFO @ Sun, 21 Jun 2020 20:28:33: Done! pass1 - making usageList (165 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 11 millis CompletedMACS2peakCalling