Job ID = 6458932 SRX = SRX5775932 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:48:26 prefetch.2.10.7: 1) Downloading 'SRR8997135'... 2020-06-21T12:48:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:51:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:51:31 prefetch.2.10.7: 1) 'SRR8997135' was downloaded successfully Read 17957873 spots for SRR8997135/SRR8997135.sra Written 17957873 spots for SRR8997135/SRR8997135.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: 00:06:45 17957873 reads; of these: 17957873 (100.00%) were unpaired; of these: 807967 (4.50%) aligned 0 times 12393213 (69.01%) aligned exactly 1 time 4756693 (26.49%) aligned >1 times 95.50% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 5905908 / 17149906 = 0.3444 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 22:03:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.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 22:03:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:39: 1000000 INFO @ Sun, 21 Jun 2020 22:03:45: 2000000 INFO @ Sun, 21 Jun 2020 22:03:52: 3000000 INFO @ Sun, 21 Jun 2020 22:03:58: 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 22:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.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 22:04:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:06: 5000000 INFO @ Sun, 21 Jun 2020 22:04:09: 1000000 INFO @ Sun, 21 Jun 2020 22:04:12: 6000000 INFO @ Sun, 21 Jun 2020 22:04:16: 2000000 INFO @ Sun, 21 Jun 2020 22:04:20: 7000000 INFO @ Sun, 21 Jun 2020 22:04:23: 3000000 INFO @ Sun, 21 Jun 2020 22:04:26: 8000000 INFO @ Sun, 21 Jun 2020 22:04:29: 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 22:04:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.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 22:04:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:34: 9000000 INFO @ Sun, 21 Jun 2020 22:04:36: 5000000 INFO @ Sun, 21 Jun 2020 22:04:39: 1000000 INFO @ Sun, 21 Jun 2020 22:04:41: 10000000 INFO @ Sun, 21 Jun 2020 22:04:43: 6000000 INFO @ Sun, 21 Jun 2020 22:04:46: 2000000 INFO @ Sun, 21 Jun 2020 22:04:48: 11000000 INFO @ Sun, 21 Jun 2020 22:04:50: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:04:50: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:04:50: #1 total tags in treatment: 11243998 INFO @ Sun, 21 Jun 2020 22:04:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:50: #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 22:04:50: 7000000 INFO @ Sun, 21 Jun 2020 22:04:50: #1 tags after filtering in treatment: 11243998 INFO @ Sun, 21 Jun 2020 22:04:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:50: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:51: #2 number of paired peaks: 940 WARNING @ Sun, 21 Jun 2020 22:04:51: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Sun, 21 Jun 2020 22:04:51: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:51: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:51: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:51: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:51: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 22:04:51: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 22:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.05_model.r WARNING @ Sun, 21 Jun 2020 22:04:51: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:51: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 22:04:51: #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 22:04:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:52: 3000000 INFO @ Sun, 21 Jun 2020 22:04:57: 8000000 INFO @ Sun, 21 Jun 2020 22:04:59: 4000000 INFO @ Sun, 21 Jun 2020 22:05:04: 9000000 INFO @ Sun, 21 Jun 2020 22:05:05: 5000000 INFO @ Sun, 21 Jun 2020 22:05:11: 10000000 INFO @ Sun, 21 Jun 2020 22:05:11: 6000000 INFO @ Sun, 21 Jun 2020 22:05:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:18: 7000000 INFO @ Sun, 21 Jun 2020 22:05:18: 11000000 INFO @ Sun, 21 Jun 2020 22:05:20: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:05:20: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:05:20: #1 total tags in treatment: 11243998 INFO @ Sun, 21 Jun 2020 22:05:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:20: #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 22:05:20: #1 tags after filtering in treatment: 11243998 INFO @ Sun, 21 Jun 2020 22:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:20: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:21: #2 number of paired peaks: 940 WARNING @ Sun, 21 Jun 2020 22:05:21: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:21: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:21: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:21: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:21: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:21: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 22:05:21: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 22:05:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.10_model.r WARNING @ Sun, 21 Jun 2020 22:05:21: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:21: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 22:05:21: #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 22:05:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:24: 8000000 INFO @ Sun, 21 Jun 2020 22:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.05_summits.bed INFO @ Sun, 21 Jun 2020 22:05:27: Done! pass1 - making usageList (708 chroms): 2 millis pass2 - checking and writing primary data (2205 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:30: 9000000 INFO @ Sun, 21 Jun 2020 22:05:36: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:05:43: 11000000 INFO @ Sun, 21 Jun 2020 22:05:44: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:05:44: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:05:44: #1 total tags in treatment: 11243998 INFO @ Sun, 21 Jun 2020 22:05:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:44: #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 22:05:45: #1 tags after filtering in treatment: 11243998 INFO @ Sun, 21 Jun 2020 22:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:45: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:46: #2 number of paired peaks: 940 WARNING @ Sun, 21 Jun 2020 22:05:46: Fewer paired peaks (940) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 940 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:46: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:46: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:46: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:46: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:46: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 22:05:46: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 21 Jun 2020 22:05:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.20_model.r WARNING @ Sun, 21 Jun 2020 22:05:46: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:46: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 21 Jun 2020 22:05:46: #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 22:05:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.10_summits.bed INFO @ Sun, 21 Jun 2020 22:05:58: Done! pass1 - making usageList (596 chroms): 1 millis pass2 - checking and writing primary data (1670 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:06:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775932/SRX5775932.20_summits.bed INFO @ Sun, 21 Jun 2020 22:06:24: Done! pass1 - making usageList (432 chroms): 1 millis pass2 - checking and writing primary data (1157 records, 4 fields): 14 millis CompletedMACS2peakCalling