Job ID = 6457537 SRX = SRX4669029 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:54:18 prefetch.2.10.7: 1) Downloading 'SRR7817554'... 2020-06-21T11:54:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:55:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:55:57 prefetch.2.10.7: 'SRR7817554' is valid 2020-06-21T11:55:57 prefetch.2.10.7: 1) 'SRR7817554' was downloaded successfully 2020-06-21T11:55:57 prefetch.2.10.7: 'SRR7817554' has 0 unresolved dependencies Read 22465149 spots for SRR7817554/SRR7817554.sra Written 22465149 spots for SRR7817554/SRR7817554.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: 00:04:45 22465149 reads; of these: 22465149 (100.00%) were unpaired; of these: 4936993 (21.98%) aligned 0 times 15444016 (68.75%) aligned exactly 1 time 2084140 (9.28%) aligned >1 times 78.02% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 12202063 / 17528156 = 0.6961 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 21:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.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 21:04:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:04:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:04:42: 1000000 INFO @ Sun, 21 Jun 2020 21:04:48: 2000000 INFO @ Sun, 21 Jun 2020 21:04:54: 3000000 INFO @ Sun, 21 Jun 2020 21:05:01: 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 21:05:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.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 21:05:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:05:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:05:07: 5000000 INFO @ Sun, 21 Jun 2020 21:05:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:05:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:05:09: #1 total tags in treatment: 5326093 INFO @ Sun, 21 Jun 2020 21:05:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:05:09: #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 21:05:10: #1 tags after filtering in treatment: 5325999 INFO @ Sun, 21 Jun 2020 21:05:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:05:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:05:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:05:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:05:10: #2 number of paired peaks: 980 WARNING @ Sun, 21 Jun 2020 21:05:10: Fewer paired peaks (980) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 980 pairs to build model! INFO @ Sun, 21 Jun 2020 21:05:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:05:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:05:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:05:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:05:10: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 21:05:10: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 21:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.05_model.r WARNING @ Sun, 21 Jun 2020 21:05:10: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:05:10: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sun, 21 Jun 2020 21:05:10: #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 21:05:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:05:12: 1000000 INFO @ Sun, 21 Jun 2020 21:05:19: 2000000 INFO @ Sun, 21 Jun 2020 21:05:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:25: 3000000 INFO @ Sun, 21 Jun 2020 21:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.05_summits.bed INFO @ Sun, 21 Jun 2020 21:05:27: Done! pass1 - making usageList (421 chroms): 2 millis pass2 - checking and writing primary data (4841 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:05:31: 4000000 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 21:05:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.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 21:05:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:05:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:05:38: 5000000 INFO @ Sun, 21 Jun 2020 21:05:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:05:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:05:40: #1 total tags in treatment: 5326093 INFO @ Sun, 21 Jun 2020 21:05:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:05:40: #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 21:05:41: #1 tags after filtering in treatment: 5325999 INFO @ Sun, 21 Jun 2020 21:05:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:05:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:05:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:05:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:05:41: #2 number of paired peaks: 980 WARNING @ Sun, 21 Jun 2020 21:05:41: Fewer paired peaks (980) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 980 pairs to build model! INFO @ Sun, 21 Jun 2020 21:05:41: start model_add_line... INFO @ Sun, 21 Jun 2020 21:05:41: start X-correlation... INFO @ Sun, 21 Jun 2020 21:05:41: end of X-cor INFO @ Sun, 21 Jun 2020 21:05:41: #2 finished! INFO @ Sun, 21 Jun 2020 21:05:41: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 21:05:41: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 21:05:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.10_model.r WARNING @ Sun, 21 Jun 2020 21:05:41: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:05:41: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sun, 21 Jun 2020 21:05:41: #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 21:05:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:05:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:05:42: 1000000 INFO @ Sun, 21 Jun 2020 21:05:49: 2000000 INFO @ Sun, 21 Jun 2020 21:05:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:55: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.10_summits.bed INFO @ Sun, 21 Jun 2020 21:05:59: Done! pass1 - making usageList (250 chroms): 1 millis pass2 - checking and writing primary data (1890 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:06:01: 4000000 INFO @ Sun, 21 Jun 2020 21:06:08: 5000000 INFO @ Sun, 21 Jun 2020 21:06:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:06:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:06:10: #1 total tags in treatment: 5326093 INFO @ Sun, 21 Jun 2020 21:06:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:06:10: #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 21:06:10: #1 tags after filtering in treatment: 5325999 INFO @ Sun, 21 Jun 2020 21:06:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:06:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:06:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:06:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:06:11: #2 number of paired peaks: 980 WARNING @ Sun, 21 Jun 2020 21:06:11: Fewer paired peaks (980) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 980 pairs to build model! INFO @ Sun, 21 Jun 2020 21:06:11: start model_add_line... INFO @ Sun, 21 Jun 2020 21:06:11: start X-correlation... INFO @ Sun, 21 Jun 2020 21:06:11: end of X-cor INFO @ Sun, 21 Jun 2020 21:06:11: #2 finished! INFO @ Sun, 21 Jun 2020 21:06:11: #2 predicted fragment length is 95 bps INFO @ Sun, 21 Jun 2020 21:06:11: #2 alternative fragment length(s) may be 95 bps INFO @ Sun, 21 Jun 2020 21:06:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.20_model.r WARNING @ Sun, 21 Jun 2020 21:06:11: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:06:11: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sun, 21 Jun 2020 21:06:11: #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 21:06:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:06:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:06:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:06:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:06:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:06:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669029/SRX4669029.20_summits.bed INFO @ Sun, 21 Jun 2020 21:06:29: Done! pass1 - making usageList (116 chroms): 0 millis pass2 - checking and writing primary data (459 records, 4 fields): 20 millis CompletedMACS2peakCalling