Job ID = 14171503 SRX = SRX10000683 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: 00:04:26 23191887 reads; of these: 23191887 (100.00%) were unpaired; of these: 21753108 (93.80%) aligned 0 times 1021763 (4.41%) aligned exactly 1 time 417016 (1.80%) aligned >1 times 6.20% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 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_rmdupse_core] 202856 / 1438779 = 0.1410 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:56:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.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 @ Sat, 11 Dec 2021 11:56:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:56:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:56:11: 1000000 INFO @ Sat, 11 Dec 2021 11:56:13: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 11:56:13: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 11:56:13: #1 total tags in treatment: 1235923 INFO @ Sat, 11 Dec 2021 11:56:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:56:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:56:13: #1 tags after filtering in treatment: 1235515 INFO @ Sat, 11 Dec 2021 11:56:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:56:13: #1 finished! INFO @ Sat, 11 Dec 2021 11:56:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:56:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:56:13: #2 number of paired peaks: 1791 INFO @ Sat, 11 Dec 2021 11:56:13: start model_add_line... INFO @ Sat, 11 Dec 2021 11:56:13: start X-correlation... INFO @ Sat, 11 Dec 2021 11:56:13: end of X-cor INFO @ Sat, 11 Dec 2021 11:56:13: #2 finished! INFO @ Sat, 11 Dec 2021 11:56:13: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 11:56:13: #2 alternative fragment length(s) may be 102,587 bps INFO @ Sat, 11 Dec 2021 11:56:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.05_model.r WARNING @ Sat, 11 Dec 2021 11:56:13: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:56:13: #2 You may need to consider one of the other alternative d(s): 102,587 WARNING @ Sat, 11 Dec 2021 11:56:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:56:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:56:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:56:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.05_summits.bed INFO @ Sat, 11 Dec 2021 11:56:18: Done! pass1 - making usageList (273 chroms): 1 millis pass2 - checking and writing primary data (516 records, 4 fields): 8 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:56:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.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 @ Sat, 11 Dec 2021 11:56:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:56:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:56:41: 1000000 INFO @ Sat, 11 Dec 2021 11:56:42: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 11:56:42: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 11:56:42: #1 total tags in treatment: 1235923 INFO @ Sat, 11 Dec 2021 11:56:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:56:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:56:43: #1 tags after filtering in treatment: 1235515 INFO @ Sat, 11 Dec 2021 11:56:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:56:43: #1 finished! INFO @ Sat, 11 Dec 2021 11:56:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:56:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:56:43: #2 number of paired peaks: 1791 INFO @ Sat, 11 Dec 2021 11:56:43: start model_add_line... INFO @ Sat, 11 Dec 2021 11:56:43: start X-correlation... INFO @ Sat, 11 Dec 2021 11:56:43: end of X-cor INFO @ Sat, 11 Dec 2021 11:56:43: #2 finished! INFO @ Sat, 11 Dec 2021 11:56:43: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 11:56:43: #2 alternative fragment length(s) may be 102,587 bps INFO @ Sat, 11 Dec 2021 11:56:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.10_model.r WARNING @ Sat, 11 Dec 2021 11:56:43: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:56:43: #2 You may need to consider one of the other alternative d(s): 102,587 WARNING @ Sat, 11 Dec 2021 11:56:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:56:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:56:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:56:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:56:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:56:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.10_summits.bed INFO @ Sat, 11 Dec 2021 11:56:47: Done! pass1 - making usageList (147 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:57:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.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 @ Sat, 11 Dec 2021 11:57:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:57:04: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:57:11: 1000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:57:13: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 11:57:13: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 11:57:13: #1 total tags in treatment: 1235923 INFO @ Sat, 11 Dec 2021 11:57:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:57:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:57:13: #1 tags after filtering in treatment: 1235515 INFO @ Sat, 11 Dec 2021 11:57:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:57:13: #1 finished! INFO @ Sat, 11 Dec 2021 11:57:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:57:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:57:13: #2 number of paired peaks: 1791 INFO @ Sat, 11 Dec 2021 11:57:13: start model_add_line... INFO @ Sat, 11 Dec 2021 11:57:13: start X-correlation... INFO @ Sat, 11 Dec 2021 11:57:13: end of X-cor INFO @ Sat, 11 Dec 2021 11:57:13: #2 finished! INFO @ Sat, 11 Dec 2021 11:57:13: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 11:57:13: #2 alternative fragment length(s) may be 102,587 bps INFO @ Sat, 11 Dec 2021 11:57:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.20_model.r WARNING @ Sat, 11 Dec 2021 11:57:13: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:57:13: #2 You may need to consider one of the other alternative d(s): 102,587 WARNING @ Sat, 11 Dec 2021 11:57:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:57:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:57:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:57:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:57:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:57:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000683/SRX10000683.20_summits.bed INFO @ Sat, 11 Dec 2021 11:57:18: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (89 records, 4 fields): 5 millis CompletedMACS2peakCalling