Job ID = 16437781 SRX = SRX12261330 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26995928 spots for SRR15972586/SRR15972586.sra Written 26995928 spots for SRR15972586/SRR15972586.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438085 ("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: 00:17:44 26995928 reads; of these: 26995928 (100.00%) were unpaired; of these: 1224803 (4.54%) aligned 0 times 15220195 (56.38%) aligned exactly 1 time 10550930 (39.08%) aligned >1 times 95.46% overall alignment rate Time searching: 00:17:44 Overall time: 00:17:44 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] 17226977 / 25771125 = 0.6685 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 13:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.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 13:32:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:32:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:32:55: 1000000 INFO @ Tue, 02 Aug 2022 13:33:00: 2000000 INFO @ Tue, 02 Aug 2022 13:33:05: 3000000 INFO @ Tue, 02 Aug 2022 13:33:11: 4000000 INFO @ Tue, 02 Aug 2022 13:33:16: 5000000 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 13:33:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.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 13:33:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:33:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:33:21: 6000000 INFO @ Tue, 02 Aug 2022 13:33:25: 1000000 INFO @ Tue, 02 Aug 2022 13:33:27: 7000000 INFO @ Tue, 02 Aug 2022 13:33:30: 2000000 INFO @ Tue, 02 Aug 2022 13:33:33: 8000000 INFO @ Tue, 02 Aug 2022 13:33:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:33:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:33:36: #1 total tags in treatment: 8544148 INFO @ Tue, 02 Aug 2022 13:33:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:33:36: #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 13:33:36: #1 tags after filtering in treatment: 8544148 INFO @ Tue, 02 Aug 2022 13:33:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:33:36: #1 finished! INFO @ Tue, 02 Aug 2022 13:33:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:33:36: 3000000 INFO @ Tue, 02 Aug 2022 13:33:36: #2 number of paired peaks: 1420 INFO @ Tue, 02 Aug 2022 13:33:36: start model_add_line... INFO @ Tue, 02 Aug 2022 13:33:37: start X-correlation... INFO @ Tue, 02 Aug 2022 13:33:37: end of X-cor INFO @ Tue, 02 Aug 2022 13:33:37: #2 finished! INFO @ Tue, 02 Aug 2022 13:33:37: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:33:37: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 13:33:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.05_model.r WARNING @ Tue, 02 Aug 2022 13:33:37: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:33:37: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 13:33:37: #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 13:33:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:33:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:33:41: 4000000 INFO @ Tue, 02 Aug 2022 13:33:47: 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 13:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.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 13:33:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:33:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:33:52: 6000000 INFO @ Tue, 02 Aug 2022 13:33:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:33:56: 1000000 INFO @ Tue, 02 Aug 2022 13:33:58: 7000000 INFO @ Tue, 02 Aug 2022 13:34:02: 2000000 INFO @ Tue, 02 Aug 2022 13:34:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:34:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:34:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.05_summits.bed INFO @ Tue, 02 Aug 2022 13:34:04: 8000000 INFO @ Tue, 02 Aug 2022 13:34:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8573 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:34:07: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:34:07: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:34:07: #1 total tags in treatment: 8544148 INFO @ Tue, 02 Aug 2022 13:34:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:34:07: #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 13:34:07: #1 tags after filtering in treatment: 8544148 INFO @ Tue, 02 Aug 2022 13:34:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:34:07: #1 finished! INFO @ Tue, 02 Aug 2022 13:34:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:34:08: #2 number of paired peaks: 1420 INFO @ Tue, 02 Aug 2022 13:34:08: start model_add_line... INFO @ Tue, 02 Aug 2022 13:34:08: start X-correlation... INFO @ Tue, 02 Aug 2022 13:34:08: end of X-cor INFO @ Tue, 02 Aug 2022 13:34:08: #2 finished! INFO @ Tue, 02 Aug 2022 13:34:08: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:34:08: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 13:34:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.10_model.r WARNING @ Tue, 02 Aug 2022 13:34:08: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:34:08: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 13:34:08: #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 13:34:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:34:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:34:09: 3000000 INFO @ Tue, 02 Aug 2022 13:34:15: 4000000 INFO @ Tue, 02 Aug 2022 13:34:22: 5000000 INFO @ Tue, 02 Aug 2022 13:34:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:34:28: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:34:34: 7000000 INFO @ Tue, 02 Aug 2022 13:34:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:34:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:34:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.10_summits.bed INFO @ Tue, 02 Aug 2022 13:34:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3951 records, 4 fields): 196 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:34:41: 8000000 INFO @ Tue, 02 Aug 2022 13:34:44: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:34:44: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:34:44: #1 total tags in treatment: 8544148 INFO @ Tue, 02 Aug 2022 13:34:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:34:44: #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 13:34:44: #1 tags after filtering in treatment: 8544148 INFO @ Tue, 02 Aug 2022 13:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:34:44: #1 finished! INFO @ Tue, 02 Aug 2022 13:34:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:34:45: #2 number of paired peaks: 1420 INFO @ Tue, 02 Aug 2022 13:34:45: start model_add_line... INFO @ Tue, 02 Aug 2022 13:34:45: start X-correlation... INFO @ Tue, 02 Aug 2022 13:34:45: end of X-cor INFO @ Tue, 02 Aug 2022 13:34:45: #2 finished! INFO @ Tue, 02 Aug 2022 13:34:45: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:34:45: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 13:34:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.20_model.r WARNING @ Tue, 02 Aug 2022 13:34:45: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:34:45: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 13:34:45: #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 13:34:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:34:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:35:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:35:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:35:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:35:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261330/SRX12261330.20_summits.bed INFO @ Tue, 02 Aug 2022 13:35:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1406 records, 4 fields): 16 millis CompletedMACS2peakCalling