Job ID = 16438025 SRX = SRX14148457 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25326446 spots for SRR17992814/SRR17992814.sra Written 25326446 spots for SRR17992814/SRR17992814.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438113 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:11 25326446 reads; of these: 25326446 (100.00%) were unpaired; of these: 1645572 (6.50%) aligned 0 times 12870650 (50.82%) aligned exactly 1 time 10810224 (42.68%) aligned >1 times 93.50% overall alignment rate Time searching: 00:18:11 Overall time: 00:18:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4685770 / 23680874 = 0.1979 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 13:46:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/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 13:46:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:46:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:46:27: 1000000 INFO @ Tue, 02 Aug 2022 13:46:37: 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 13:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/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 13:46:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:46:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:46:47: 3000000 INFO @ Tue, 02 Aug 2022 13:46:56: 1000000 INFO @ Tue, 02 Aug 2022 13:46:58: 4000000 INFO @ Tue, 02 Aug 2022 13:47:05: 2000000 INFO @ Tue, 02 Aug 2022 13:47:08: 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 13:47:15: 3000000 INFO @ Tue, 02 Aug 2022 13:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/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 13:47:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:47:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:47:19: 6000000 INFO @ Tue, 02 Aug 2022 13:47:24: 4000000 INFO @ Tue, 02 Aug 2022 13:47:27: 1000000 INFO @ Tue, 02 Aug 2022 13:47:29: 7000000 INFO @ Tue, 02 Aug 2022 13:47:34: 5000000 INFO @ Tue, 02 Aug 2022 13:47:37: 2000000 INFO @ Tue, 02 Aug 2022 13:47:40: 8000000 INFO @ Tue, 02 Aug 2022 13:47:43: 6000000 INFO @ Tue, 02 Aug 2022 13:47:48: 3000000 INFO @ Tue, 02 Aug 2022 13:47:50: 9000000 INFO @ Tue, 02 Aug 2022 13:47:53: 7000000 INFO @ Tue, 02 Aug 2022 13:47:58: 4000000 INFO @ Tue, 02 Aug 2022 13:48:01: 10000000 INFO @ Tue, 02 Aug 2022 13:48:03: 8000000 INFO @ Tue, 02 Aug 2022 13:48:09: 5000000 INFO @ Tue, 02 Aug 2022 13:48:11: 11000000 INFO @ Tue, 02 Aug 2022 13:48:12: 9000000 INFO @ Tue, 02 Aug 2022 13:48:19: 6000000 INFO @ Tue, 02 Aug 2022 13:48:21: 12000000 INFO @ Tue, 02 Aug 2022 13:48:22: 10000000 INFO @ Tue, 02 Aug 2022 13:48:30: 7000000 INFO @ Tue, 02 Aug 2022 13:48:31: 11000000 INFO @ Tue, 02 Aug 2022 13:48:32: 13000000 INFO @ Tue, 02 Aug 2022 13:48:40: 8000000 INFO @ Tue, 02 Aug 2022 13:48:40: 12000000 INFO @ Tue, 02 Aug 2022 13:48:42: 14000000 INFO @ Tue, 02 Aug 2022 13:48:50: 13000000 INFO @ Tue, 02 Aug 2022 13:48:51: 9000000 INFO @ Tue, 02 Aug 2022 13:48:53: 15000000 INFO @ Tue, 02 Aug 2022 13:48:59: 14000000 INFO @ Tue, 02 Aug 2022 13:49:02: 10000000 INFO @ Tue, 02 Aug 2022 13:49:04: 16000000 INFO @ Tue, 02 Aug 2022 13:49:09: 15000000 INFO @ Tue, 02 Aug 2022 13:49:12: 11000000 INFO @ Tue, 02 Aug 2022 13:49:14: 17000000 INFO @ Tue, 02 Aug 2022 13:49:19: 16000000 INFO @ Tue, 02 Aug 2022 13:49:23: 12000000 INFO @ Tue, 02 Aug 2022 13:49:24: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:49:28: 17000000 INFO @ Tue, 02 Aug 2022 13:49:33: 13000000 INFO @ Tue, 02 Aug 2022 13:49:35: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:49:35: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:49:35: #1 total tags in treatment: 18995104 INFO @ Tue, 02 Aug 2022 13:49:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:49:35: #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 13:49:35: #1 tags after filtering in treatment: 18995104 INFO @ Tue, 02 Aug 2022 13:49:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:49:35: #1 finished! INFO @ Tue, 02 Aug 2022 13:49:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:49:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:49:36: #2 number of paired peaks: 1160 INFO @ Tue, 02 Aug 2022 13:49:36: start model_add_line... INFO @ Tue, 02 Aug 2022 13:49:37: start X-correlation... INFO @ Tue, 02 Aug 2022 13:49:37: end of X-cor INFO @ Tue, 02 Aug 2022 13:49:37: #2 finished! INFO @ Tue, 02 Aug 2022 13:49:37: #2 predicted fragment length is 96 bps INFO @ Tue, 02 Aug 2022 13:49:37: #2 alternative fragment length(s) may be 4,96 bps INFO @ Tue, 02 Aug 2022 13:49:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.05_model.r WARNING @ Tue, 02 Aug 2022 13:49:37: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:49:37: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Tue, 02 Aug 2022 13:49:37: #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 13:49:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:49:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:49:38: 18000000 INFO @ Tue, 02 Aug 2022 13:49:44: 14000000 INFO @ Tue, 02 Aug 2022 13:49:47: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:49:47: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:49:47: #1 total tags in treatment: 18995104 INFO @ Tue, 02 Aug 2022 13:49:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:49:47: #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 13:49:47: #1 tags after filtering in treatment: 18995104 INFO @ Tue, 02 Aug 2022 13:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:49:47: #1 finished! INFO @ Tue, 02 Aug 2022 13:49:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:49:49: #2 number of paired peaks: 1160 INFO @ Tue, 02 Aug 2022 13:49:49: start model_add_line... INFO @ Tue, 02 Aug 2022 13:49:49: start X-correlation... INFO @ Tue, 02 Aug 2022 13:49:49: end of X-cor INFO @ Tue, 02 Aug 2022 13:49:49: #2 finished! INFO @ Tue, 02 Aug 2022 13:49:49: #2 predicted fragment length is 96 bps INFO @ Tue, 02 Aug 2022 13:49:49: #2 alternative fragment length(s) may be 4,96 bps INFO @ Tue, 02 Aug 2022 13:49:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.10_model.r WARNING @ Tue, 02 Aug 2022 13:49:49: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:49:49: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Tue, 02 Aug 2022 13:49:49: #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 13:49:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:49:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:49:54: 15000000 INFO @ Tue, 02 Aug 2022 13:50:05: 16000000 INFO @ Tue, 02 Aug 2022 13:50:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:50:15: 17000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:50:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:50:26: 18000000 INFO @ Tue, 02 Aug 2022 13:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:50:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:50:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.05_summits.bed INFO @ Tue, 02 Aug 2022 13:50:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8764 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:50:36: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:50:36: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:50:36: #1 total tags in treatment: 18995104 INFO @ Tue, 02 Aug 2022 13:50:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:50:36: #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 13:50:36: #1 tags after filtering in treatment: 18995104 INFO @ Tue, 02 Aug 2022 13:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:50:36: #1 finished! INFO @ Tue, 02 Aug 2022 13:50:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:50:38: #2 number of paired peaks: 1160 INFO @ Tue, 02 Aug 2022 13:50:38: start model_add_line... INFO @ Tue, 02 Aug 2022 13:50:38: start X-correlation... INFO @ Tue, 02 Aug 2022 13:50:38: end of X-cor INFO @ Tue, 02 Aug 2022 13:50:38: #2 finished! INFO @ Tue, 02 Aug 2022 13:50:38: #2 predicted fragment length is 96 bps INFO @ Tue, 02 Aug 2022 13:50:38: #2 alternative fragment length(s) may be 4,96 bps INFO @ Tue, 02 Aug 2022 13:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.20_model.r WARNING @ Tue, 02 Aug 2022 13:50:38: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:50:38: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Tue, 02 Aug 2022 13:50:38: #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 13:50:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:50:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.10_summits.bed INFO @ Tue, 02 Aug 2022 13:50:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5482 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:51:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:51:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:51:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:51:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148457/SRX14148457.20_summits.bed INFO @ Tue, 02 Aug 2022 13:51:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2949 records, 4 fields): 32 millis CompletedMACS2peakCalling