Job ID = 6458952 SRX = SRX5827821 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:44:10 prefetch.2.10.7: 1) Downloading 'SRR9051572'... 2020-06-21T12:44:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:49:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:49:47 prefetch.2.10.7: 1) 'SRR9051572' was downloaded successfully 2020-06-21T12:49:47 prefetch.2.10.7: 'SRR9051572' has 0 unresolved dependencies Read 38788443 spots for SRR9051572/SRR9051572.sra Written 38788443 spots for SRR9051572/SRR9051572.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: 00:09:08 38788443 reads; of these: 38788443 (100.00%) were unpaired; of these: 8009484 (20.65%) aligned 0 times 24226234 (62.46%) aligned exactly 1 time 6552725 (16.89%) aligned >1 times 79.35% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 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 16 files... [bam_rmdupse_core] 17508065 / 30778959 = 0.5688 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 22:08:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.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 22:08:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:11: 1000000 INFO @ Sun, 21 Jun 2020 22:08:16: 2000000 INFO @ Sun, 21 Jun 2020 22:08:22: 3000000 INFO @ Sun, 21 Jun 2020 22:08:27: 4000000 INFO @ Sun, 21 Jun 2020 22:08:33: 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 22:08:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.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 22:08:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:08:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:08:38: 6000000 INFO @ Sun, 21 Jun 2020 22:08:41: 1000000 INFO @ Sun, 21 Jun 2020 22:08:44: 7000000 INFO @ Sun, 21 Jun 2020 22:08:47: 2000000 INFO @ Sun, 21 Jun 2020 22:08:50: 8000000 INFO @ Sun, 21 Jun 2020 22:08:52: 3000000 INFO @ Sun, 21 Jun 2020 22:08:56: 9000000 INFO @ Sun, 21 Jun 2020 22:08:58: 4000000 INFO @ Sun, 21 Jun 2020 22:09:02: 10000000 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 22:09:04: 5000000 INFO @ Sun, 21 Jun 2020 22:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.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 22:09:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:08: 11000000 INFO @ Sun, 21 Jun 2020 22:09:09: 6000000 INFO @ Sun, 21 Jun 2020 22:09:11: 1000000 INFO @ Sun, 21 Jun 2020 22:09:14: 12000000 INFO @ Sun, 21 Jun 2020 22:09:16: 7000000 INFO @ Sun, 21 Jun 2020 22:09:17: 2000000 INFO @ Sun, 21 Jun 2020 22:09:20: 13000000 INFO @ Sun, 21 Jun 2020 22:09:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:09:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:09:21: #1 total tags in treatment: 13270894 INFO @ Sun, 21 Jun 2020 22:09:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:21: #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 22:09:22: 8000000 INFO @ Sun, 21 Jun 2020 22:09:22: #1 tags after filtering in treatment: 13270893 INFO @ Sun, 21 Jun 2020 22:09:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:23: 3000000 INFO @ Sun, 21 Jun 2020 22:09:23: #2 number of paired peaks: 832 WARNING @ Sun, 21 Jun 2020 22:09:23: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Sun, 21 Jun 2020 22:09:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:23: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:09:23: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 21 Jun 2020 22:09:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.05_model.r WARNING @ Sun, 21 Jun 2020 22:09:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:09:23: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 21 Jun 2020 22:09:23: #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 22:09:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:09:27: 9000000 INFO @ Sun, 21 Jun 2020 22:09:29: 4000000 INFO @ Sun, 21 Jun 2020 22:09:33: 10000000 INFO @ Sun, 21 Jun 2020 22:09:35: 5000000 INFO @ Sun, 21 Jun 2020 22:09:40: 11000000 INFO @ Sun, 21 Jun 2020 22:09:40: 6000000 INFO @ Sun, 21 Jun 2020 22:09:46: 12000000 INFO @ Sun, 21 Jun 2020 22:09:46: 7000000 INFO @ Sun, 21 Jun 2020 22:09:52: 13000000 INFO @ Sun, 21 Jun 2020 22:09:52: 8000000 INFO @ Sun, 21 Jun 2020 22:09:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:09:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:09:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:09:54: #1 total tags in treatment: 13270894 INFO @ Sun, 21 Jun 2020 22:09:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:54: #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 22:09:54: #1 tags after filtering in treatment: 13270893 INFO @ Sun, 21 Jun 2020 22:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:54: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:55: #2 number of paired peaks: 832 WARNING @ Sun, 21 Jun 2020 22:09:55: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Sun, 21 Jun 2020 22:09:55: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:55: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:55: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:55: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:55: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:09:55: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 21 Jun 2020 22:09:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.10_model.r WARNING @ Sun, 21 Jun 2020 22:09:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:09:55: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 21 Jun 2020 22:09:55: #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 22:09:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:09:58: 9000000 INFO @ Sun, 21 Jun 2020 22:10:04: 10000000 INFO @ Sun, 21 Jun 2020 22:10:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:10:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:10:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.05_summits.bed INFO @ Sun, 21 Jun 2020 22:10:07: Done! pass1 - making usageList (699 chroms): 1 millis pass2 - checking and writing primary data (3640 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:10:11: 11000000 INFO @ Sun, 21 Jun 2020 22:10:17: 12000000 INFO @ Sun, 21 Jun 2020 22:10:22: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:10:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:10:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:10:24: #1 total tags in treatment: 13270894 INFO @ Sun, 21 Jun 2020 22:10:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:24: #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 22:10:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:10:25: #1 tags after filtering in treatment: 13270893 INFO @ Sun, 21 Jun 2020 22:10:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:25: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:26: #2 number of paired peaks: 832 WARNING @ Sun, 21 Jun 2020 22:10:26: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:26: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:26: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:26: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:26: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:26: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:10:26: #2 alternative fragment length(s) may be 3,48 bps INFO @ Sun, 21 Jun 2020 22:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.20_model.r WARNING @ Sun, 21 Jun 2020 22:10:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:10:26: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Sun, 21 Jun 2020 22:10:26: #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 22:10:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.10_summits.bed INFO @ Sun, 21 Jun 2020 22:10:39: Done! pass1 - making usageList (552 chroms): 1 millis pass2 - checking and writing primary data (2321 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:10:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:11:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827821/SRX5827821.20_summits.bed INFO @ Sun, 21 Jun 2020 22:11:11: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (878 records, 4 fields): 13 millis CompletedMACS2peakCalling