Job ID = 10166148 SRX = SRX7723689 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:04:41 14707499 reads; of these: 14707499 (100.00%) were unpaired; of these: 3115098 (21.18%) aligned 0 times 10021581 (68.14%) aligned exactly 1 time 1570820 (10.68%) aligned >1 times 78.82% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 2704860 / 11592401 = 0.2333 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 @ Thu, 08 Oct 2020 20:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.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 @ Thu, 08 Oct 2020 20:41:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:23: 1000000 INFO @ Thu, 08 Oct 2020 20:41:30: 2000000 INFO @ Thu, 08 Oct 2020 20:41:36: 3000000 INFO @ Thu, 08 Oct 2020 20:41:43: 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 @ Thu, 08 Oct 2020 20:41:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.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 @ Thu, 08 Oct 2020 20:41:46: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:46: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:50: 5000000 INFO @ Thu, 08 Oct 2020 20:41:53: 1000000 INFO @ Thu, 08 Oct 2020 20:41:57: 6000000 INFO @ Thu, 08 Oct 2020 20:42:00: 2000000 INFO @ Thu, 08 Oct 2020 20:42:04: 7000000 INFO @ Thu, 08 Oct 2020 20:42:07: 3000000 INFO @ Thu, 08 Oct 2020 20:42:11: 8000000 INFO @ Thu, 08 Oct 2020 20:42:14: 4000000 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 @ Thu, 08 Oct 2020 20:42:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.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 @ Thu, 08 Oct 2020 20:42:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:18: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:42:18: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:42:18: #1 total tags in treatment: 8887541 INFO @ Thu, 08 Oct 2020 20:42:18: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:42:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:42:18: #1 tags after filtering in treatment: 8887308 INFO @ Thu, 08 Oct 2020 20:42:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:42:18: #1 finished! INFO @ Thu, 08 Oct 2020 20:42:18: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:42:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:42:19: #2 number of paired peaks: 1179 INFO @ Thu, 08 Oct 2020 20:42:19: start model_add_line... INFO @ Thu, 08 Oct 2020 20:42:19: start X-correlation... INFO @ Thu, 08 Oct 2020 20:42:19: end of X-cor INFO @ Thu, 08 Oct 2020 20:42:19: #2 finished! INFO @ Thu, 08 Oct 2020 20:42:19: #2 predicted fragment length is 107 bps INFO @ Thu, 08 Oct 2020 20:42:19: #2 alternative fragment length(s) may be 107 bps INFO @ Thu, 08 Oct 2020 20:42:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05_model.r WARNING @ Thu, 08 Oct 2020 20:42:19: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:42:19: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Thu, 08 Oct 2020 20:42:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:42:19: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:42:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:42:21: 5000000 INFO @ Thu, 08 Oct 2020 20:42:24: 1000000 INFO @ Thu, 08 Oct 2020 20:42:29: 6000000 INFO @ Thu, 08 Oct 2020 20:42:31: 2000000 INFO @ Thu, 08 Oct 2020 20:42:36: 7000000 INFO @ Thu, 08 Oct 2020 20:42:37: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:42:38: 3000000 INFO @ Thu, 08 Oct 2020 20:42:43: 8000000 INFO @ Thu, 08 Oct 2020 20:42:45: 4000000 INFO @ Thu, 08 Oct 2020 20:42:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:42:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:42:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05_summits.bed INFO @ Thu, 08 Oct 2020 20:42:48: Done! pass1 - making usageList (289 chroms): 3 millis pass2 - checking and writing primary data (17888 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:42:50: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:42:50: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:42:50: #1 total tags in treatment: 8887541 INFO @ Thu, 08 Oct 2020 20:42:50: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:42:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:42:50: #1 tags after filtering in treatment: 8887308 INFO @ Thu, 08 Oct 2020 20:42:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:42:50: #1 finished! INFO @ Thu, 08 Oct 2020 20:42:50: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:42:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:42:51: #2 number of paired peaks: 1179 INFO @ Thu, 08 Oct 2020 20:42:51: start model_add_line... INFO @ Thu, 08 Oct 2020 20:42:51: start X-correlation... INFO @ Thu, 08 Oct 2020 20:42:51: end of X-cor INFO @ Thu, 08 Oct 2020 20:42:51: #2 finished! INFO @ Thu, 08 Oct 2020 20:42:51: #2 predicted fragment length is 107 bps INFO @ Thu, 08 Oct 2020 20:42:51: #2 alternative fragment length(s) may be 107 bps INFO @ Thu, 08 Oct 2020 20:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10_model.r WARNING @ Thu, 08 Oct 2020 20:42:51: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:42:51: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Thu, 08 Oct 2020 20:42:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:42:51: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:42:52: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:42:58: 6000000 INFO @ Thu, 08 Oct 2020 20:43:05: 7000000 INFO @ Thu, 08 Oct 2020 20:43:10: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:43:11: 8000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:43:17: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:43:17: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:43:17: #1 total tags in treatment: 8887541 INFO @ Thu, 08 Oct 2020 20:43:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:43:17: #1 tags after filtering in treatment: 8887308 INFO @ Thu, 08 Oct 2020 20:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:17: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:18: #2 number of paired peaks: 1179 INFO @ Thu, 08 Oct 2020 20:43:18: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:18: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:18: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:18: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:18: #2 predicted fragment length is 107 bps INFO @ Thu, 08 Oct 2020 20:43:18: #2 alternative fragment length(s) may be 107 bps INFO @ Thu, 08 Oct 2020 20:43:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20_model.r WARNING @ Thu, 08 Oct 2020 20:43:18: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:43:18: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Thu, 08 Oct 2020 20:43:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:43:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:43:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10_summits.bed INFO @ Thu, 08 Oct 2020 20:43:20: Done! pass1 - making usageList (222 chroms): 2 millis pass2 - checking and writing primary data (7537 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:43:37: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20_summits.bed INFO @ Thu, 08 Oct 2020 20:43:47: Done! pass1 - making usageList (172 chroms): 1 millis pass2 - checking and writing primary data (1936 records, 4 fields): 9 millis CompletedMACS2peakCalling