Job ID = 6454981 SRX = SRX2618520 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:51:25 prefetch.2.10.7: 1) Downloading 'SRR5319074'... 2020-06-21T09:51:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:57 prefetch.2.10.7: 'SRR5319074' is valid 2020-06-21T09:52:57 prefetch.2.10.7: 1) 'SRR5319074' was downloaded successfully 2020-06-21T09:52:57 prefetch.2.10.7: 'SRR5319074' has 0 unresolved dependencies Read 15644699 spots for SRR5319074/SRR5319074.sra Written 15644699 spots for SRR5319074/SRR5319074.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: 00:04:21 15644699 reads; of these: 15644699 (100.00%) were unpaired; of these: 965973 (6.17%) aligned 0 times 10989725 (70.25%) aligned exactly 1 time 3689001 (23.58%) aligned >1 times 93.83% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 2065835 / 14678726 = 0.1407 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 19:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.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 19:02:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:24: 1000000 INFO @ Sun, 21 Jun 2020 19:02:30: 2000000 INFO @ Sun, 21 Jun 2020 19:02:36: 3000000 INFO @ Sun, 21 Jun 2020 19:02:42: 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 19:02:47: 5000000 INFO @ Sun, 21 Jun 2020 19:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.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 19:02:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:54: 6000000 INFO @ Sun, 21 Jun 2020 19:02:56: 1000000 INFO @ Sun, 21 Jun 2020 19:03:01: 7000000 INFO @ Sun, 21 Jun 2020 19:03:03: 2000000 INFO @ Sun, 21 Jun 2020 19:03:09: 8000000 INFO @ Sun, 21 Jun 2020 19:03:10: 3000000 INFO @ Sun, 21 Jun 2020 19:03:16: 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 19:03:18: 4000000 INFO @ Sun, 21 Jun 2020 19:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.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 19:03:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:23: 10000000 INFO @ Sun, 21 Jun 2020 19:03:25: 5000000 INFO @ Sun, 21 Jun 2020 19:03:26: 1000000 INFO @ Sun, 21 Jun 2020 19:03:31: 11000000 INFO @ Sun, 21 Jun 2020 19:03:33: 6000000 INFO @ Sun, 21 Jun 2020 19:03:34: 2000000 INFO @ Sun, 21 Jun 2020 19:03:39: 12000000 INFO @ Sun, 21 Jun 2020 19:03:40: 7000000 INFO @ Sun, 21 Jun 2020 19:03:42: 3000000 INFO @ Sun, 21 Jun 2020 19:03:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:43: #1 total tags in treatment: 12612891 INFO @ Sun, 21 Jun 2020 19:03:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:43: #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 19:03:44: #1 tags after filtering in treatment: 12612891 INFO @ Sun, 21 Jun 2020 19:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:45: #2 number of paired peaks: 797 WARNING @ Sun, 21 Jun 2020 19:03:45: Fewer paired peaks (797) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 797 pairs to build model! INFO @ Sun, 21 Jun 2020 19:03:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:45: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 19:03:45: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 19:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.05_model.r WARNING @ Sun, 21 Jun 2020 19:03:45: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:03:45: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 19:03:45: #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 19:03:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:48: 8000000 INFO @ Sun, 21 Jun 2020 19:03:49: 4000000 INFO @ Sun, 21 Jun 2020 19:03:55: 9000000 INFO @ Sun, 21 Jun 2020 19:03:56: 5000000 INFO @ Sun, 21 Jun 2020 19:04:02: 10000000 INFO @ Sun, 21 Jun 2020 19:04:03: 6000000 INFO @ Sun, 21 Jun 2020 19:04:10: 11000000 INFO @ Sun, 21 Jun 2020 19:04:10: 7000000 INFO @ Sun, 21 Jun 2020 19:04:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:17: 12000000 INFO @ Sun, 21 Jun 2020 19:04:17: 8000000 INFO @ Sun, 21 Jun 2020 19:04:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:21: #1 total tags in treatment: 12612891 INFO @ Sun, 21 Jun 2020 19:04:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:21: #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 19:04:22: #1 tags after filtering in treatment: 12612891 INFO @ Sun, 21 Jun 2020 19:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:23: #2 number of paired peaks: 797 WARNING @ Sun, 21 Jun 2020 19:04:23: Fewer paired peaks (797) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 797 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:23: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 19:04:23: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 19:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.10_model.r WARNING @ Sun, 21 Jun 2020 19:04:23: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:23: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 19:04:23: #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 19:04:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.05_summits.bed INFO @ Sun, 21 Jun 2020 19:04:24: Done! INFO @ Sun, 21 Jun 2020 19:04:24: 9000000 pass1 - making usageList (597 chroms): 2 millis pass2 - checking and writing primary data (5916 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:04:31: 10000000 INFO @ Sun, 21 Jun 2020 19:04:37: 11000000 INFO @ Sun, 21 Jun 2020 19:04:43: 12000000 INFO @ Sun, 21 Jun 2020 19:04:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:47: #1 total tags in treatment: 12612891 INFO @ Sun, 21 Jun 2020 19:04:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:47: #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 19:04:47: #1 tags after filtering in treatment: 12612891 INFO @ Sun, 21 Jun 2020 19:04:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:48: #2 number of paired peaks: 797 WARNING @ Sun, 21 Jun 2020 19:04:48: Fewer paired peaks (797) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 797 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:48: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 19:04:48: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 19:04:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.20_model.r WARNING @ Sun, 21 Jun 2020 19:04:48: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:48: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 19:04:48: #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 19:04:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:05:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:03: Done! pass1 - making usageList (509 chroms): 2 millis pass2 - checking and writing primary data (3188 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618520/SRX2618520.20_summits.bed INFO @ Sun, 21 Jun 2020 19:05:27: Done! pass1 - making usageList (367 chroms): 2 millis pass2 - checking and writing primary data (1180 records, 4 fields): 11 millis CompletedMACS2peakCalling