Job ID = 6458867 SRX = SRX5717037 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:52:37 prefetch.2.10.7: 1) Downloading 'SRR8936398'... 2020-06-21T12:52:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:56:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:56:07 prefetch.2.10.7: 'SRR8936398' is valid 2020-06-21T12:56:07 prefetch.2.10.7: 1) 'SRR8936398' was downloaded successfully Read 20772231 spots for SRR8936398/SRR8936398.sra Written 20772231 spots for SRR8936398/SRR8936398.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: 00:05:22 20772231 reads; of these: 20772231 (100.00%) were unpaired; of these: 2515506 (12.11%) aligned 0 times 12620389 (60.76%) aligned exactly 1 time 5636336 (27.13%) aligned >1 times 87.89% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 4494771 / 18256725 = 0.2462 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 22:06:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.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 22:06:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:43: 1000000 INFO @ Sun, 21 Jun 2020 22:06:47: 2000000 INFO @ Sun, 21 Jun 2020 22:06:52: 3000000 INFO @ Sun, 21 Jun 2020 22:06:57: 4000000 INFO @ Sun, 21 Jun 2020 22:07:02: 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 22:07:07: 6000000 INFO @ Sun, 21 Jun 2020 22:07:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.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 22:07:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:13: 7000000 INFO @ Sun, 21 Jun 2020 22:07:13: 1000000 INFO @ Sun, 21 Jun 2020 22:07:18: 8000000 INFO @ Sun, 21 Jun 2020 22:07:18: 2000000 INFO @ Sun, 21 Jun 2020 22:07:23: 9000000 INFO @ Sun, 21 Jun 2020 22:07:23: 3000000 INFO @ Sun, 21 Jun 2020 22:07:28: 10000000 INFO @ Sun, 21 Jun 2020 22:07:29: 4000000 INFO @ Sun, 21 Jun 2020 22:07:33: 11000000 INFO @ Sun, 21 Jun 2020 22:07:34: 5000000 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 22:07:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.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 22:07:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:39: 6000000 INFO @ Sun, 21 Jun 2020 22:07:39: 12000000 INFO @ Sun, 21 Jun 2020 22:07:43: 1000000 INFO @ Sun, 21 Jun 2020 22:07:44: 7000000 INFO @ Sun, 21 Jun 2020 22:07:44: 13000000 INFO @ Sun, 21 Jun 2020 22:07:48: 2000000 INFO @ Sun, 21 Jun 2020 22:07:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:07:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:07:49: #1 total tags in treatment: 13761954 INFO @ Sun, 21 Jun 2020 22:07:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:07:49: #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 22:07:49: #1 tags after filtering in treatment: 13761877 INFO @ Sun, 21 Jun 2020 22:07:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:07:49: #1 finished! INFO @ Sun, 21 Jun 2020 22:07:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:07:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:07:49: 8000000 INFO @ Sun, 21 Jun 2020 22:07:50: #2 number of paired peaks: 400 WARNING @ Sun, 21 Jun 2020 22:07:50: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Sun, 21 Jun 2020 22:07:50: start model_add_line... INFO @ Sun, 21 Jun 2020 22:07:50: start X-correlation... INFO @ Sun, 21 Jun 2020 22:07:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:07:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:07:50: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 22:07:50: #2 alternative fragment length(s) may be 53,100,177,559,585 bps INFO @ Sun, 21 Jun 2020 22:07:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.05_model.r WARNING @ Sun, 21 Jun 2020 22:07:50: #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 22:07:50: #2 You may need to consider one of the other alternative d(s): 53,100,177,559,585 WARNING @ Sun, 21 Jun 2020 22:07:50: #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 22:07:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:07:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:07:54: 3000000 INFO @ Sun, 21 Jun 2020 22:07:55: 9000000 INFO @ Sun, 21 Jun 2020 22:07:59: 4000000 INFO @ Sun, 21 Jun 2020 22:08:00: 10000000 INFO @ Sun, 21 Jun 2020 22:08:04: 5000000 INFO @ Sun, 21 Jun 2020 22:08:05: 11000000 INFO @ Sun, 21 Jun 2020 22:08:09: 6000000 INFO @ Sun, 21 Jun 2020 22:08:11: 12000000 INFO @ Sun, 21 Jun 2020 22:08:15: 7000000 INFO @ Sun, 21 Jun 2020 22:08:16: 13000000 INFO @ Sun, 21 Jun 2020 22:08:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:20: 8000000 INFO @ Sun, 21 Jun 2020 22:08:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:08:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:08:21: #1 total tags in treatment: 13761954 INFO @ Sun, 21 Jun 2020 22:08:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:08:21: #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 22:08:21: #1 tags after filtering in treatment: 13761877 INFO @ Sun, 21 Jun 2020 22:08:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:08:21: #1 finished! INFO @ Sun, 21 Jun 2020 22:08:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:08:22: #2 number of paired peaks: 400 WARNING @ Sun, 21 Jun 2020 22:08:22: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Sun, 21 Jun 2020 22:08:22: start model_add_line... INFO @ Sun, 21 Jun 2020 22:08:22: start X-correlation... INFO @ Sun, 21 Jun 2020 22:08:22: end of X-cor INFO @ Sun, 21 Jun 2020 22:08:22: #2 finished! INFO @ Sun, 21 Jun 2020 22:08:22: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 22:08:22: #2 alternative fragment length(s) may be 53,100,177,559,585 bps INFO @ Sun, 21 Jun 2020 22:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.10_model.r WARNING @ Sun, 21 Jun 2020 22:08:22: #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 22:08:22: #2 You may need to consider one of the other alternative d(s): 53,100,177,559,585 WARNING @ Sun, 21 Jun 2020 22:08:22: #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 22:08:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:08:25: 9000000 INFO @ Sun, 21 Jun 2020 22:08:30: 10000000 INFO @ Sun, 21 Jun 2020 22:08:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:08:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:08:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.05_summits.bed INFO @ Sun, 21 Jun 2020 22:08:32: Done! pass1 - making usageList (461 chroms): 1 millis pass2 - checking and writing primary data (1959 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:08:35: 11000000 INFO @ Sun, 21 Jun 2020 22:08:40: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:08:45: 13000000 INFO @ Sun, 21 Jun 2020 22:08:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:08:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:08:49: #1 total tags in treatment: 13761954 INFO @ Sun, 21 Jun 2020 22:08:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:08:49: #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 22:08:50: #1 tags after filtering in treatment: 13761877 INFO @ Sun, 21 Jun 2020 22:08:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:08:50: #1 finished! INFO @ Sun, 21 Jun 2020 22:08:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:08:51: #2 number of paired peaks: 400 WARNING @ Sun, 21 Jun 2020 22:08:51: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Sun, 21 Jun 2020 22:08:51: start model_add_line... INFO @ Sun, 21 Jun 2020 22:08:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:08:51: start X-correlation... INFO @ Sun, 21 Jun 2020 22:08:51: end of X-cor INFO @ Sun, 21 Jun 2020 22:08:51: #2 finished! INFO @ Sun, 21 Jun 2020 22:08:51: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 22:08:51: #2 alternative fragment length(s) may be 53,100,177,559,585 bps INFO @ Sun, 21 Jun 2020 22:08:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.20_model.r WARNING @ Sun, 21 Jun 2020 22:08:51: #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 22:08:51: #2 You may need to consider one of the other alternative d(s): 53,100,177,559,585 WARNING @ Sun, 21 Jun 2020 22:08:51: #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 22:08:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:09:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.10_summits.bed INFO @ Sun, 21 Jun 2020 22:09:05: Done! pass1 - making usageList (289 chroms): 1 millis pass2 - checking and writing primary data (671 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:09:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:09:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:09:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:09:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717037/SRX5717037.20_summits.bed INFO @ Sun, 21 Jun 2020 22:09:32: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 5 millis CompletedMACS2peakCalling