Job ID = 6454986 SRX = SRX2618525 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:46:10 prefetch.2.10.7: 1) Downloading 'SRR5319079'... 2020-06-21T09:46:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:47:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:47:27 prefetch.2.10.7: 'SRR5319079' is valid 2020-06-21T09:47:27 prefetch.2.10.7: 1) 'SRR5319079' was downloaded successfully 2020-06-21T09:47:27 prefetch.2.10.7: 'SRR5319079' has 0 unresolved dependencies Read 14084117 spots for SRR5319079/SRR5319079.sra Written 14084117 spots for SRR5319079/SRR5319079.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: 00:03:57 14084117 reads; of these: 14084117 (100.00%) were unpaired; of these: 734546 (5.22%) aligned 0 times 9278164 (65.88%) aligned exactly 1 time 4071407 (28.91%) aligned >1 times 94.78% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 1845721 / 13349571 = 0.1383 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 18:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.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 18:55:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:56: 1000000 INFO @ Sun, 21 Jun 2020 18:56:02: 2000000 INFO @ Sun, 21 Jun 2020 18:56:07: 3000000 INFO @ Sun, 21 Jun 2020 18:56:13: 4000000 INFO @ Sun, 21 Jun 2020 18:56:18: 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 18:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.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 18:56:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:24: 6000000 INFO @ Sun, 21 Jun 2020 18:56:28: 1000000 INFO @ Sun, 21 Jun 2020 18:56:30: 7000000 INFO @ Sun, 21 Jun 2020 18:56:35: 2000000 INFO @ Sun, 21 Jun 2020 18:56:36: 8000000 INFO @ Sun, 21 Jun 2020 18:56:42: 3000000 INFO @ Sun, 21 Jun 2020 18:56:43: 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 18:56:49: 4000000 INFO @ Sun, 21 Jun 2020 18:56:50: 10000000 INFO @ Sun, 21 Jun 2020 18:56:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.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 18:56:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:56: 5000000 INFO @ Sun, 21 Jun 2020 18:56:57: 11000000 INFO @ Sun, 21 Jun 2020 18:56:59: 1000000 INFO @ Sun, 21 Jun 2020 18:57:00: #1 tag size is determined as 48 bps INFO @ Sun, 21 Jun 2020 18:57:00: #1 tag size = 48 INFO @ Sun, 21 Jun 2020 18:57:00: #1 total tags in treatment: 11503850 INFO @ Sun, 21 Jun 2020 18:57:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:00: #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 18:57:01: #1 tags after filtering in treatment: 11503850 INFO @ Sun, 21 Jun 2020 18:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:01: #2 number of paired peaks: 876 WARNING @ Sun, 21 Jun 2020 18:57:01: Fewer paired peaks (876) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 876 pairs to build model! INFO @ Sun, 21 Jun 2020 18:57:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:02: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:02: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:02: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 18:57:02: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 18:57:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.05_model.r WARNING @ Sun, 21 Jun 2020 18:57:02: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:57:02: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 18:57:02: #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 18:57:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:03: 6000000 INFO @ Sun, 21 Jun 2020 18:57:05: 2000000 INFO @ Sun, 21 Jun 2020 18:57:10: 7000000 INFO @ Sun, 21 Jun 2020 18:57:12: 3000000 INFO @ Sun, 21 Jun 2020 18:57:17: 8000000 INFO @ Sun, 21 Jun 2020 18:57:18: 4000000 INFO @ Sun, 21 Jun 2020 18:57:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:25: 9000000 INFO @ Sun, 21 Jun 2020 18:57:25: 5000000 INFO @ Sun, 21 Jun 2020 18:57:31: 6000000 INFO @ Sun, 21 Jun 2020 18:57:32: 10000000 INFO @ Sun, 21 Jun 2020 18:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.05_summits.bed INFO @ Sun, 21 Jun 2020 18:57:35: Done! pass1 - making usageList (645 chroms): 1 millis pass2 - checking and writing primary data (2232 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:38: 7000000 INFO @ Sun, 21 Jun 2020 18:57:39: 11000000 INFO @ Sun, 21 Jun 2020 18:57:43: #1 tag size is determined as 48 bps INFO @ Sun, 21 Jun 2020 18:57:43: #1 tag size = 48 INFO @ Sun, 21 Jun 2020 18:57:43: #1 total tags in treatment: 11503850 INFO @ Sun, 21 Jun 2020 18:57:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:43: #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 18:57:43: #1 tags after filtering in treatment: 11503850 INFO @ Sun, 21 Jun 2020 18:57:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:44: #2 number of paired peaks: 876 WARNING @ Sun, 21 Jun 2020 18:57:44: Fewer paired peaks (876) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 876 pairs to build model! INFO @ Sun, 21 Jun 2020 18:57:44: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:44: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:44: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:44: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:44: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 18:57:44: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 18:57:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.10_model.r WARNING @ Sun, 21 Jun 2020 18:57:44: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:57:44: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 18:57:44: #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 18:57:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:45: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:57:51: 9000000 INFO @ Sun, 21 Jun 2020 18:57:56: 10000000 INFO @ Sun, 21 Jun 2020 18:58:02: 11000000 INFO @ Sun, 21 Jun 2020 18:58:05: #1 tag size is determined as 48 bps INFO @ Sun, 21 Jun 2020 18:58:05: #1 tag size = 48 INFO @ Sun, 21 Jun 2020 18:58:05: #1 total tags in treatment: 11503850 INFO @ Sun, 21 Jun 2020 18:58:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:05: #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 18:58:05: #1 tags after filtering in treatment: 11503850 INFO @ Sun, 21 Jun 2020 18:58:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:06: #2 number of paired peaks: 876 WARNING @ Sun, 21 Jun 2020 18:58:06: Fewer paired peaks (876) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 876 pairs to build model! INFO @ Sun, 21 Jun 2020 18:58:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:06: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 18:58:06: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 18:58:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.20_model.r WARNING @ Sun, 21 Jun 2020 18:58:06: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:06: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 18:58:06: #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 18:58:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:58:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.10_summits.bed INFO @ Sun, 21 Jun 2020 18:58:18: Done! pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (1922 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618525/SRX2618525.20_summits.bed INFO @ Sun, 21 Jun 2020 18:58:40: Done! pass1 - making usageList (415 chroms): 1 millis pass2 - checking and writing primary data (1204 records, 4 fields): 13 millis CompletedMACS2peakCalling