Job ID = 16438113 SRX = SRX14148457 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: 00:16:04 25326446 reads; of these: 25326446 (100.00%) were unpaired; of these: 1901988 (7.51%) aligned 0 times 13849048 (54.68%) aligned exactly 1 time 9575410 (37.81%) aligned >1 times 92.49% overall alignment rate Time searching: 00:16:04 Overall time: 00:16:04 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 12 files... [bam_rmdupse_core] 6177289 / 23424458 = 0.2637 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:07:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.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 @ Tue, 02 Aug 2022 14:07:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:07:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:07:23: 1000000 INFO @ Tue, 02 Aug 2022 14:07:33: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.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 @ Tue, 02 Aug 2022 14:07:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:07:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:07:43: 3000000 INFO @ Tue, 02 Aug 2022 14:07:50: 1000000 INFO @ Tue, 02 Aug 2022 14:07:53: 4000000 INFO @ Tue, 02 Aug 2022 14:08:00: 2000000 INFO @ Tue, 02 Aug 2022 14:08:03: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.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 @ Tue, 02 Aug 2022 14:08:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:08:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:08:10: 3000000 INFO @ Tue, 02 Aug 2022 14:08:14: 6000000 INFO @ Tue, 02 Aug 2022 14:08:19: 1000000 INFO @ Tue, 02 Aug 2022 14:08:20: 4000000 INFO @ Tue, 02 Aug 2022 14:08:24: 7000000 INFO @ Tue, 02 Aug 2022 14:08:28: 2000000 INFO @ Tue, 02 Aug 2022 14:08:30: 5000000 INFO @ Tue, 02 Aug 2022 14:08:35: 8000000 INFO @ Tue, 02 Aug 2022 14:08:37: 3000000 INFO @ Tue, 02 Aug 2022 14:08:41: 6000000 INFO @ Tue, 02 Aug 2022 14:08:45: 4000000 INFO @ Tue, 02 Aug 2022 14:08:45: 9000000 INFO @ Tue, 02 Aug 2022 14:08:51: 7000000 INFO @ Tue, 02 Aug 2022 14:08:54: 5000000 INFO @ Tue, 02 Aug 2022 14:08:56: 10000000 INFO @ Tue, 02 Aug 2022 14:09:01: 8000000 INFO @ Tue, 02 Aug 2022 14:09:03: 6000000 INFO @ Tue, 02 Aug 2022 14:09:05: 11000000 INFO @ Tue, 02 Aug 2022 14:09:11: 9000000 INFO @ Tue, 02 Aug 2022 14:09:12: 7000000 INFO @ Tue, 02 Aug 2022 14:09:15: 12000000 INFO @ Tue, 02 Aug 2022 14:09:21: 8000000 INFO @ Tue, 02 Aug 2022 14:09:22: 10000000 INFO @ Tue, 02 Aug 2022 14:09:25: 13000000 INFO @ Tue, 02 Aug 2022 14:09:31: 9000000 INFO @ Tue, 02 Aug 2022 14:09:32: 11000000 INFO @ Tue, 02 Aug 2022 14:09:34: 14000000 INFO @ Tue, 02 Aug 2022 14:09:41: 10000000 INFO @ Tue, 02 Aug 2022 14:09:42: 12000000 INFO @ Tue, 02 Aug 2022 14:09:45: 15000000 INFO @ Tue, 02 Aug 2022 14:09:50: 11000000 INFO @ Tue, 02 Aug 2022 14:09:52: 13000000 INFO @ Tue, 02 Aug 2022 14:09:56: 16000000 INFO @ Tue, 02 Aug 2022 14:10:00: 12000000 INFO @ Tue, 02 Aug 2022 14:10:02: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:10:06: 17000000 INFO @ Tue, 02 Aug 2022 14:10:09: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:10:09: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:10:09: #1 total tags in treatment: 17247169 INFO @ Tue, 02 Aug 2022 14:10:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:10:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:10:09: #1 tags after filtering in treatment: 17247072 INFO @ Tue, 02 Aug 2022 14:10:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:10:09: #1 finished! INFO @ Tue, 02 Aug 2022 14:10:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:10:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:10:10: 13000000 INFO @ Tue, 02 Aug 2022 14:10:11: #2 number of paired peaks: 2377 INFO @ Tue, 02 Aug 2022 14:10:11: start model_add_line... INFO @ Tue, 02 Aug 2022 14:10:11: start X-correlation... INFO @ Tue, 02 Aug 2022 14:10:12: end of X-cor INFO @ Tue, 02 Aug 2022 14:10:12: #2 finished! INFO @ Tue, 02 Aug 2022 14:10:12: #2 predicted fragment length is 89 bps INFO @ Tue, 02 Aug 2022 14:10:12: #2 alternative fragment length(s) may be 3,89 bps INFO @ Tue, 02 Aug 2022 14:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.05_model.r WARNING @ Tue, 02 Aug 2022 14:10:12: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:10:12: #2 You may need to consider one of the other alternative d(s): 3,89 WARNING @ Tue, 02 Aug 2022 14:10:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:10:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:10:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:10:12: 15000000 INFO @ Tue, 02 Aug 2022 14:10:19: 14000000 INFO @ Tue, 02 Aug 2022 14:10:23: 16000000 INFO @ Tue, 02 Aug 2022 14:10:28: 15000000 INFO @ Tue, 02 Aug 2022 14:10:33: 17000000 INFO @ Tue, 02 Aug 2022 14:10:35: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:10:35: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:10:35: #1 total tags in treatment: 17247169 INFO @ Tue, 02 Aug 2022 14:10:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:10:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:10:36: #1 tags after filtering in treatment: 17247072 INFO @ Tue, 02 Aug 2022 14:10:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:10:36: #1 finished! INFO @ Tue, 02 Aug 2022 14:10:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:10:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:10:38: #2 number of paired peaks: 2377 INFO @ Tue, 02 Aug 2022 14:10:38: start model_add_line... INFO @ Tue, 02 Aug 2022 14:10:38: start X-correlation... INFO @ Tue, 02 Aug 2022 14:10:38: end of X-cor INFO @ Tue, 02 Aug 2022 14:10:38: #2 finished! INFO @ Tue, 02 Aug 2022 14:10:38: #2 predicted fragment length is 89 bps INFO @ Tue, 02 Aug 2022 14:10:38: #2 alternative fragment length(s) may be 3,89 bps INFO @ Tue, 02 Aug 2022 14:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.10_model.r WARNING @ Tue, 02 Aug 2022 14:10:38: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:10:38: #2 You may need to consider one of the other alternative d(s): 3,89 WARNING @ Tue, 02 Aug 2022 14:10:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:10:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:10:38: 16000000 INFO @ Tue, 02 Aug 2022 14:10:47: 17000000 INFO @ Tue, 02 Aug 2022 14:10:50: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:10:50: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:10:50: #1 total tags in treatment: 17247169 INFO @ Tue, 02 Aug 2022 14:10:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:10:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:10:51: #1 tags after filtering in treatment: 17247072 INFO @ Tue, 02 Aug 2022 14:10:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:10:51: #1 finished! INFO @ Tue, 02 Aug 2022 14:10:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:10:53: #2 number of paired peaks: 2377 INFO @ Tue, 02 Aug 2022 14:10:53: start model_add_line... INFO @ Tue, 02 Aug 2022 14:10:53: start X-correlation... INFO @ Tue, 02 Aug 2022 14:10:53: end of X-cor INFO @ Tue, 02 Aug 2022 14:10:53: #2 finished! INFO @ Tue, 02 Aug 2022 14:10:53: #2 predicted fragment length is 89 bps INFO @ Tue, 02 Aug 2022 14:10:53: #2 alternative fragment length(s) may be 3,89 bps INFO @ Tue, 02 Aug 2022 14:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.20_model.r WARNING @ Tue, 02 Aug 2022 14:10:53: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:10:53: #2 You may need to consider one of the other alternative d(s): 3,89 WARNING @ Tue, 02 Aug 2022 14:10:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:10:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:10:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:11:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:11:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:11:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:11:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.05_summits.bed INFO @ Tue, 02 Aug 2022 14:11:24: Done! pass1 - making usageList (701 chroms): 2 millis pass2 - checking and writing primary data (4647 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:11:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:11:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.10_summits.bed INFO @ Tue, 02 Aug 2022 14:11:50: Done! pass1 - making usageList (635 chroms): 4 millis pass2 - checking and writing primary data (2741 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX14148457/SRX14148457.20_summits.bed INFO @ Tue, 02 Aug 2022 14:12:05: Done! pass1 - making usageList (574 chroms): 2 millis pass2 - checking and writing primary data (1794 records, 4 fields): 47 millis CompletedMACS2peakCalling