Job ID = 6455694 SRX = SRX287995 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:13:36 prefetch.2.10.7: 1) Downloading 'SRR870184'... 2020-06-21T10:13:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:15:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:15:47 prefetch.2.10.7: 1) 'SRR870184' was downloaded successfully Read 17570684 spots for SRR870184/SRR870184.sra Written 17570684 spots for SRR870184/SRR870184.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: 00:05:41 17570684 reads; of these: 17570684 (100.00%) were unpaired; of these: 1164885 (6.63%) aligned 0 times 11092332 (63.13%) aligned exactly 1 time 5313467 (30.24%) aligned >1 times 93.37% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 3298511 / 16405799 = 0.2011 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 19:26:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.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 19:26:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:57: 1000000 INFO @ Sun, 21 Jun 2020 19:27:03: 2000000 INFO @ Sun, 21 Jun 2020 19:27:08: 3000000 INFO @ Sun, 21 Jun 2020 19:27:15: 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 19:27:21: 5000000 INFO @ Sun, 21 Jun 2020 19:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.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 19:27:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:27: 6000000 INFO @ Sun, 21 Jun 2020 19:27:28: 1000000 INFO @ Sun, 21 Jun 2020 19:27:34: 7000000 INFO @ Sun, 21 Jun 2020 19:27:35: 2000000 INFO @ Sun, 21 Jun 2020 19:27:41: 8000000 INFO @ Sun, 21 Jun 2020 19:27:42: 3000000 INFO @ Sun, 21 Jun 2020 19:27:48: 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 19:27:49: 4000000 INFO @ Sun, 21 Jun 2020 19:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.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 19:27:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:55: 10000000 INFO @ Sun, 21 Jun 2020 19:27:57: 5000000 INFO @ Sun, 21 Jun 2020 19:27:59: 1000000 INFO @ Sun, 21 Jun 2020 19:28:03: 11000000 INFO @ Sun, 21 Jun 2020 19:28:05: 6000000 INFO @ Sun, 21 Jun 2020 19:28:07: 2000000 INFO @ Sun, 21 Jun 2020 19:28:10: 12000000 INFO @ Sun, 21 Jun 2020 19:28:12: 7000000 INFO @ Sun, 21 Jun 2020 19:28:15: 3000000 INFO @ Sun, 21 Jun 2020 19:28:18: 13000000 INFO @ Sun, 21 Jun 2020 19:28:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:19: #1 total tags in treatment: 13107288 INFO @ Sun, 21 Jun 2020 19:28:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:19: #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 19:28:20: #1 tags after filtering in treatment: 13107288 INFO @ Sun, 21 Jun 2020 19:28:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:20: 8000000 INFO @ Sun, 21 Jun 2020 19:28:21: #2 number of paired peaks: 563 WARNING @ Sun, 21 Jun 2020 19:28:21: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sun, 21 Jun 2020 19:28:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:21: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:28:21: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:28:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.05_model.r WARNING @ Sun, 21 Jun 2020 19:28:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:21: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:28:21: #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 19:28:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:23: 4000000 INFO @ Sun, 21 Jun 2020 19:28:27: 9000000 INFO @ Sun, 21 Jun 2020 19:28:31: 5000000 INFO @ Sun, 21 Jun 2020 19:28:35: 10000000 INFO @ Sun, 21 Jun 2020 19:28:39: 6000000 INFO @ Sun, 21 Jun 2020 19:28:42: 11000000 INFO @ Sun, 21 Jun 2020 19:28:47: 7000000 INFO @ Sun, 21 Jun 2020 19:28:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:50: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:28:54: 8000000 INFO @ Sun, 21 Jun 2020 19:28:57: 13000000 INFO @ Sun, 21 Jun 2020 19:28:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:58: #1 total tags in treatment: 13107288 INFO @ Sun, 21 Jun 2020 19:28:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:58: #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 19:28:58: #1 tags after filtering in treatment: 13107288 INFO @ Sun, 21 Jun 2020 19:28:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:59: #2 number of paired peaks: 563 WARNING @ Sun, 21 Jun 2020 19:28:59: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sun, 21 Jun 2020 19:28:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:59: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:28:59: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.10_model.r WARNING @ Sun, 21 Jun 2020 19:28:59: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:59: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:28:59: #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 19:28:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.05_summits.bed INFO @ Sun, 21 Jun 2020 19:29:01: Done! pass1 - making usageList (606 chroms): 1 millis pass2 - checking and writing primary data (2310 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:29:02: 9000000 INFO @ Sun, 21 Jun 2020 19:29:09: 10000000 INFO @ Sun, 21 Jun 2020 19:29:17: 11000000 INFO @ Sun, 21 Jun 2020 19:29:24: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:29:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:31: 13000000 INFO @ Sun, 21 Jun 2020 19:29:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:32: #1 total tags in treatment: 13107288 INFO @ Sun, 21 Jun 2020 19:29:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:32: #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 19:29:32: #1 tags after filtering in treatment: 13107288 INFO @ Sun, 21 Jun 2020 19:29:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:33: #2 number of paired peaks: 563 WARNING @ Sun, 21 Jun 2020 19:29:33: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Sun, 21 Jun 2020 19:29:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:33: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:29:33: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:29:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.20_model.r WARNING @ Sun, 21 Jun 2020 19:29:33: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:29:33: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:29:33: #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 19:29:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.10_summits.bed INFO @ Sun, 21 Jun 2020 19:29:40: Done! pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (1845 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287995/SRX287995.20_summits.bed INFO @ Sun, 21 Jun 2020 19:30:13: Done! pass1 - making usageList (307 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 9 millis CompletedMACS2peakCalling