Job ID = 16438038 SRX = SRX12261345 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17560870 spots for SRR15972601/SRR15972601.sra Written 17560870 spots for SRR15972601/SRR15972601.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438109 ("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: 00:11:13 17560870 reads; of these: 17560870 (100.00%) were unpaired; of these: 614312 (3.50%) aligned 0 times 9139734 (52.05%) aligned exactly 1 time 7806824 (44.46%) aligned >1 times 96.50% overall alignment rate Time searching: 00:11:14 Overall time: 00:11:14 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 8 files... [bam_rmdupse_core] 10582380 / 16946558 = 0.6245 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 13:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.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 13:37:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:37:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:37:50: 1000000 INFO @ Tue, 02 Aug 2022 13:37:56: 2000000 INFO @ Tue, 02 Aug 2022 13:38:02: 3000000 INFO @ Tue, 02 Aug 2022 13:38:08: 4000000 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 13:38:14: 5000000 INFO @ Tue, 02 Aug 2022 13:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.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 13:38:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:38:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:38:20: 6000000 INFO @ Tue, 02 Aug 2022 13:38:21: 1000000 INFO @ Tue, 02 Aug 2022 13:38:22: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:38:22: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:38:22: #1 total tags in treatment: 6364178 INFO @ Tue, 02 Aug 2022 13:38:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:38:22: #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 13:38:22: #1 tags after filtering in treatment: 6364178 INFO @ Tue, 02 Aug 2022 13:38:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:38:22: #1 finished! INFO @ Tue, 02 Aug 2022 13:38:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:38:23: #2 number of paired peaks: 1321 INFO @ Tue, 02 Aug 2022 13:38:23: start model_add_line... INFO @ Tue, 02 Aug 2022 13:38:23: start X-correlation... INFO @ Tue, 02 Aug 2022 13:38:23: end of X-cor INFO @ Tue, 02 Aug 2022 13:38:23: #2 finished! INFO @ Tue, 02 Aug 2022 13:38:23: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:38:23: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 13:38:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.05_model.r WARNING @ Tue, 02 Aug 2022 13:38:23: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:38:23: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 13:38:23: #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 13:38:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:38:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:38:28: 2000000 INFO @ Tue, 02 Aug 2022 13:38:34: 3000000 INFO @ Tue, 02 Aug 2022 13:38:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:38:40: 4000000 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 13:38:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:38:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.05_summits.bed INFO @ Tue, 02 Aug 2022 13:38:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6789 records, 4 fields): 112 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:38:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.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 13:38:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:38:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:38:47: 5000000 INFO @ Tue, 02 Aug 2022 13:38:53: 1000000 INFO @ Tue, 02 Aug 2022 13:38:54: 6000000 INFO @ Tue, 02 Aug 2022 13:38:57: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:38:57: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:38:57: #1 total tags in treatment: 6364178 INFO @ Tue, 02 Aug 2022 13:38:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:38:57: #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 13:38:57: #1 tags after filtering in treatment: 6364178 INFO @ Tue, 02 Aug 2022 13:38:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:38:57: #1 finished! INFO @ Tue, 02 Aug 2022 13:38:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:38:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:38:57: #2 number of paired peaks: 1321 INFO @ Tue, 02 Aug 2022 13:38:57: start model_add_line... INFO @ Tue, 02 Aug 2022 13:38:57: start X-correlation... INFO @ Tue, 02 Aug 2022 13:38:57: end of X-cor INFO @ Tue, 02 Aug 2022 13:38:57: #2 finished! INFO @ Tue, 02 Aug 2022 13:38:57: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:38:57: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 13:38:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.10_model.r WARNING @ Tue, 02 Aug 2022 13:38:57: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:38:57: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 13:38:57: #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 13:38:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:39:01: 2000000 INFO @ Tue, 02 Aug 2022 13:39:08: 3000000 INFO @ Tue, 02 Aug 2022 13:39:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:39:15: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:39:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:39:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:39:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.10_summits.bed INFO @ Tue, 02 Aug 2022 13:39:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3218 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:39:22: 5000000 INFO @ Tue, 02 Aug 2022 13:39:29: 6000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:39:32: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:39:32: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:39:32: #1 total tags in treatment: 6364178 INFO @ Tue, 02 Aug 2022 13:39:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:39:32: #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 13:39:32: #1 tags after filtering in treatment: 6364178 INFO @ Tue, 02 Aug 2022 13:39:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:39:32: #1 finished! INFO @ Tue, 02 Aug 2022 13:39:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:39:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:39:32: #2 number of paired peaks: 1321 INFO @ Tue, 02 Aug 2022 13:39:32: start model_add_line... INFO @ Tue, 02 Aug 2022 13:39:32: start X-correlation... INFO @ Tue, 02 Aug 2022 13:39:32: end of X-cor INFO @ Tue, 02 Aug 2022 13:39:32: #2 finished! INFO @ Tue, 02 Aug 2022 13:39:32: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:39:32: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 13:39:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.20_model.r WARNING @ Tue, 02 Aug 2022 13:39:33: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:39:33: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 13:39:33: #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 13:39:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:39:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:39:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:39:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:39:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261345/SRX12261345.20_summits.bed INFO @ Tue, 02 Aug 2022 13:39:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1167 records, 4 fields): 45 millis CompletedMACS2peakCalling