Job ID = 14167465 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: 00:04:17 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: 00:04:17 Overall time: 00:04:17 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:29:58: # 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 @ Fri, 10 Dec 2021 12:29:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:29:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:30:05: 1000000 INFO @ Fri, 10 Dec 2021 12:30:13: 2000000 INFO @ Fri, 10 Dec 2021 12:30:20: 3000000 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 @ Fri, 10 Dec 2021 12:30:28: 4000000 INFO @ Fri, 10 Dec 2021 12:30:28: # 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 @ Fri, 10 Dec 2021 12:30:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:30:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:30:36: 5000000 INFO @ Fri, 10 Dec 2021 12:30:36: 1000000 INFO @ Fri, 10 Dec 2021 12:30:44: 6000000 INFO @ Fri, 10 Dec 2021 12:30:45: 2000000 INFO @ Fri, 10 Dec 2021 12:30:53: 3000000 INFO @ Fri, 10 Dec 2021 12:30:53: 7000000 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 @ Fri, 10 Dec 2021 12:30:58: # 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 @ Fri, 10 Dec 2021 12:30:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:30:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:31:01: 8000000 INFO @ Fri, 10 Dec 2021 12:31:01: 4000000 INFO @ Fri, 10 Dec 2021 12:31:06: 1000000 INFO @ Fri, 10 Dec 2021 12:31:09: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:31:09: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:31:09: #1 total tags in treatment: 8887541 INFO @ Fri, 10 Dec 2021 12:31:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:31:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:31:09: #1 tags after filtering in treatment: 8887308 INFO @ Fri, 10 Dec 2021 12:31:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:31:09: #1 finished! INFO @ Fri, 10 Dec 2021 12:31:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:31:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:31:10: #2 number of paired peaks: 1179 INFO @ Fri, 10 Dec 2021 12:31:10: start model_add_line... INFO @ Fri, 10 Dec 2021 12:31:10: 5000000 INFO @ Fri, 10 Dec 2021 12:31:10: start X-correlation... INFO @ Fri, 10 Dec 2021 12:31:10: end of X-cor INFO @ Fri, 10 Dec 2021 12:31:10: #2 finished! INFO @ Fri, 10 Dec 2021 12:31:10: #2 predicted fragment length is 107 bps INFO @ Fri, 10 Dec 2021 12:31:10: #2 alternative fragment length(s) may be 107 bps INFO @ Fri, 10 Dec 2021 12:31:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05_model.r WARNING @ Fri, 10 Dec 2021 12:31:10: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:31:10: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Fri, 10 Dec 2021 12:31:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:31:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:31:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:31:14: 2000000 INFO @ Fri, 10 Dec 2021 12:31:19: 6000000 INFO @ Fri, 10 Dec 2021 12:31:22: 3000000 INFO @ Fri, 10 Dec 2021 12:31:28: 7000000 INFO @ Fri, 10 Dec 2021 12:31:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:31:29: 4000000 INFO @ Fri, 10 Dec 2021 12:31:36: 8000000 INFO @ Fri, 10 Dec 2021 12:31:37: 5000000 INFO @ Fri, 10 Dec 2021 12:31:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.05_summits.bed INFO @ Fri, 10 Dec 2021 12:31:39: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (289 chroms): 3 millis pass2 - checking and writing primary data (17888 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:31:44: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:31:44: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:31:44: #1 total tags in treatment: 8887541 INFO @ Fri, 10 Dec 2021 12:31:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:31:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:31:44: #1 tags after filtering in treatment: 8887308 INFO @ Fri, 10 Dec 2021 12:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:31:44: #1 finished! INFO @ Fri, 10 Dec 2021 12:31:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:31:45: #2 number of paired peaks: 1179 INFO @ Fri, 10 Dec 2021 12:31:45: start model_add_line... INFO @ Fri, 10 Dec 2021 12:31:45: start X-correlation... INFO @ Fri, 10 Dec 2021 12:31:45: end of X-cor INFO @ Fri, 10 Dec 2021 12:31:45: #2 finished! INFO @ Fri, 10 Dec 2021 12:31:45: #2 predicted fragment length is 107 bps INFO @ Fri, 10 Dec 2021 12:31:45: #2 alternative fragment length(s) may be 107 bps INFO @ Fri, 10 Dec 2021 12:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10_model.r WARNING @ Fri, 10 Dec 2021 12:31:45: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:31:45: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Fri, 10 Dec 2021 12:31:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:31:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:31:45: 6000000 INFO @ Fri, 10 Dec 2021 12:31:52: 7000000 INFO @ Fri, 10 Dec 2021 12:31:59: 8000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:32:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:32:04: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:32:04: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:32:04: #1 total tags in treatment: 8887541 INFO @ Fri, 10 Dec 2021 12:32:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:32:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:32:05: #1 tags after filtering in treatment: 8887308 INFO @ Fri, 10 Dec 2021 12:32:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:32:05: #1 finished! INFO @ Fri, 10 Dec 2021 12:32:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:32:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:32:05: #2 number of paired peaks: 1179 INFO @ Fri, 10 Dec 2021 12:32:05: start model_add_line... INFO @ Fri, 10 Dec 2021 12:32:05: start X-correlation... INFO @ Fri, 10 Dec 2021 12:32:05: end of X-cor INFO @ Fri, 10 Dec 2021 12:32:05: #2 finished! INFO @ Fri, 10 Dec 2021 12:32:05: #2 predicted fragment length is 107 bps INFO @ Fri, 10 Dec 2021 12:32:05: #2 alternative fragment length(s) may be 107 bps INFO @ Fri, 10 Dec 2021 12:32:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20_model.r WARNING @ Fri, 10 Dec 2021 12:32:05: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:32:05: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Fri, 10 Dec 2021 12:32:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:32:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:32:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.10_summits.bed INFO @ Fri, 10 Dec 2021 12:32:13: Done! pass1 - making usageList (222 chroms): 2 millis pass2 - checking and writing primary data (7537 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:32:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:32:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:32:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:32:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723689/SRX7723689.20_summits.bed INFO @ Fri, 10 Dec 2021 12:32:34: Done! pass1 - making usageList (172 chroms): 1 millis pass2 - checking and writing primary data (1936 records, 4 fields): 8 millis CompletedMACS2peakCalling