Job ID = 6456894 SRX = SRX4053304 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:08:39 prefetch.2.10.7: 1) Downloading 'SRR7132409'... 2020-06-21T11:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:09:48 prefetch.2.10.7: 'SRR7132409' is valid 2020-06-21T11:09:48 prefetch.2.10.7: 1) 'SRR7132409' was downloaded successfully 2020-06-21T11:09:48 prefetch.2.10.7: 'SRR7132409' has 0 unresolved dependencies Read 13491391 spots for SRR7132409/SRR7132409.sra Written 13491391 spots for SRR7132409/SRR7132409.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: 00:04:25 13491391 reads; of these: 13491391 (100.00%) were unpaired; of these: 2557485 (18.96%) aligned 0 times 6333551 (46.95%) aligned exactly 1 time 4600355 (34.10%) aligned >1 times 81.04% overall alignment rate Time searching: 00:04:25 Overall time: 00:04:25 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] 3803043 / 10933906 = 0.3478 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 20:17:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.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 20:17:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:17:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:17:28: 1000000 INFO @ Sun, 21 Jun 2020 20:17:33: 2000000 INFO @ Sun, 21 Jun 2020 20:17:38: 3000000 INFO @ Sun, 21 Jun 2020 20:17:43: 4000000 INFO @ Sun, 21 Jun 2020 20:17:48: 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 20:17:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.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 20:17:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:17:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:17:54: 6000000 INFO @ Sun, 21 Jun 2020 20:17:58: 1000000 INFO @ Sun, 21 Jun 2020 20:17:59: 7000000 INFO @ Sun, 21 Jun 2020 20:18:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:18:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:18:00: #1 total tags in treatment: 7130863 INFO @ Sun, 21 Jun 2020 20:18:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:18:00: #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 20:18:00: #1 tags after filtering in treatment: 7130855 INFO @ Sun, 21 Jun 2020 20:18:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:18:00: #1 finished! INFO @ Sun, 21 Jun 2020 20:18:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:18:01: #2 number of paired peaks: 759 WARNING @ Sun, 21 Jun 2020 20:18:01: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Sun, 21 Jun 2020 20:18:01: start model_add_line... INFO @ Sun, 21 Jun 2020 20:18:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:18:01: end of X-cor INFO @ Sun, 21 Jun 2020 20:18:01: #2 finished! INFO @ Sun, 21 Jun 2020 20:18:01: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 20:18:01: #2 alternative fragment length(s) may be 46,594 bps INFO @ Sun, 21 Jun 2020 20:18:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.05_model.r WARNING @ Sun, 21 Jun 2020 20:18:01: #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 20:18:01: #2 You may need to consider one of the other alternative d(s): 46,594 WARNING @ Sun, 21 Jun 2020 20:18:01: #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 20:18:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:18:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:18:04: 2000000 INFO @ Sun, 21 Jun 2020 20:18:08: 3000000 INFO @ Sun, 21 Jun 2020 20:18:13: 4000000 INFO @ Sun, 21 Jun 2020 20:18:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:18:18: 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 20:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.05_summits.bed INFO @ Sun, 21 Jun 2020 20:18:23: Done! pass1 - making usageList (651 chroms): 1 millis pass2 - checking and writing primary data (2637 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:18:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.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 20:18:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:24: 6000000 INFO @ Sun, 21 Jun 2020 20:18:29: 1000000 INFO @ Sun, 21 Jun 2020 20:18:29: 7000000 INFO @ Sun, 21 Jun 2020 20:18:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:18:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:18:30: #1 total tags in treatment: 7130863 INFO @ Sun, 21 Jun 2020 20:18:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:18:30: #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 20:18:30: #1 tags after filtering in treatment: 7130855 INFO @ Sun, 21 Jun 2020 20:18:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:18:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:18:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:18:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:18:31: #2 number of paired peaks: 759 WARNING @ Sun, 21 Jun 2020 20:18:31: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Sun, 21 Jun 2020 20:18:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:18:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:18:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:18:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:18:31: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 20:18:31: #2 alternative fragment length(s) may be 46,594 bps INFO @ Sun, 21 Jun 2020 20:18:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.10_model.r WARNING @ Sun, 21 Jun 2020 20:18:31: #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 20:18:31: #2 You may need to consider one of the other alternative d(s): 46,594 WARNING @ Sun, 21 Jun 2020 20:18:31: #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 20:18:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:18:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:18:34: 2000000 INFO @ Sun, 21 Jun 2020 20:18:39: 3000000 INFO @ Sun, 21 Jun 2020 20:18:44: 4000000 INFO @ Sun, 21 Jun 2020 20:18:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:18:49: 5000000 INFO @ Sun, 21 Jun 2020 20:18:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:18:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.10_summits.bed INFO @ Sun, 21 Jun 2020 20:18:54: Done! INFO @ Sun, 21 Jun 2020 20:18:55: 6000000 pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (1571 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:19:00: 7000000 INFO @ Sun, 21 Jun 2020 20:19:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:19:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:19:01: #1 total tags in treatment: 7130863 INFO @ Sun, 21 Jun 2020 20:19:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:01: #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 20:19:01: #1 tags after filtering in treatment: 7130855 INFO @ Sun, 21 Jun 2020 20:19:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:02: #2 number of paired peaks: 759 WARNING @ Sun, 21 Jun 2020 20:19:02: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Sun, 21 Jun 2020 20:19:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:02: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:02: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 20:19:02: #2 alternative fragment length(s) may be 46,594 bps INFO @ Sun, 21 Jun 2020 20:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.20_model.r WARNING @ Sun, 21 Jun 2020 20:19:02: #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 20:19:02: #2 You may need to consider one of the other alternative d(s): 46,594 WARNING @ Sun, 21 Jun 2020 20:19:02: #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 20:19:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:19:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:19:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:19:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:19:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053304/SRX4053304.20_summits.bed INFO @ Sun, 21 Jun 2020 20:19:25: Done! pass1 - making usageList (279 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 12 millis CompletedMACS2peakCalling