Job ID = 16437630 SRX = SRX12261322 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26617520 spots for SRR15972578/SRR15972578.sra Written 26617520 spots for SRR15972578/SRR15972578.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438061 ("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: 00:17:04 26617520 reads; of these: 26617520 (100.00%) were unpaired; of these: 1005494 (3.78%) aligned 0 times 17548887 (65.93%) aligned exactly 1 time 8063139 (30.29%) aligned >1 times 96.22% overall alignment rate Time searching: 00:17:04 Overall time: 00:17:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 11400180 / 25612026 = 0.4451 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 13:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.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 13:27:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:27:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:28:05: 1000000 INFO @ Tue, 02 Aug 2022 13:28:10: 2000000 INFO @ Tue, 02 Aug 2022 13:28:17: 3000000 INFO @ Tue, 02 Aug 2022 13:28:22: 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 13:28:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.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 13:28:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:28:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:28:28: 5000000 INFO @ Tue, 02 Aug 2022 13:28:34: 1000000 INFO @ Tue, 02 Aug 2022 13:28:34: 6000000 INFO @ Tue, 02 Aug 2022 13:28:40: 2000000 INFO @ Tue, 02 Aug 2022 13:28:40: 7000000 INFO @ Tue, 02 Aug 2022 13:28:46: 3000000 INFO @ Tue, 02 Aug 2022 13:28:46: 8000000 INFO @ Tue, 02 Aug 2022 13:28:51: 4000000 INFO @ Tue, 02 Aug 2022 13:28:52: 9000000 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 13:28:58: 5000000 INFO @ Tue, 02 Aug 2022 13:28:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.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 13:28:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:28:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:28:58: 10000000 INFO @ Tue, 02 Aug 2022 13:29:03: 6000000 INFO @ Tue, 02 Aug 2022 13:29:05: 1000000 INFO @ Tue, 02 Aug 2022 13:29:05: 11000000 INFO @ Tue, 02 Aug 2022 13:29:09: 7000000 INFO @ Tue, 02 Aug 2022 13:29:12: 12000000 INFO @ Tue, 02 Aug 2022 13:29:12: 2000000 INFO @ Tue, 02 Aug 2022 13:29:15: 8000000 INFO @ Tue, 02 Aug 2022 13:29:19: 13000000 INFO @ Tue, 02 Aug 2022 13:29:19: 3000000 INFO @ Tue, 02 Aug 2022 13:29:21: 9000000 INFO @ Tue, 02 Aug 2022 13:29:26: 14000000 INFO @ Tue, 02 Aug 2022 13:29:27: 4000000 INFO @ Tue, 02 Aug 2022 13:29:27: 10000000 INFO @ Tue, 02 Aug 2022 13:29:28: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:29:28: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:29:28: #1 total tags in treatment: 14211846 INFO @ Tue, 02 Aug 2022 13:29:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:29:28: #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 13:29:28: #1 tags after filtering in treatment: 14211846 INFO @ Tue, 02 Aug 2022 13:29:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:29:28: #1 finished! INFO @ Tue, 02 Aug 2022 13:29:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:29:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:29:29: #2 number of paired peaks: 118 WARNING @ Tue, 02 Aug 2022 13:29:29: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 02 Aug 2022 13:29:29: start model_add_line... INFO @ Tue, 02 Aug 2022 13:29:29: start X-correlation... INFO @ Tue, 02 Aug 2022 13:29:29: end of X-cor INFO @ Tue, 02 Aug 2022 13:29:29: #2 finished! INFO @ Tue, 02 Aug 2022 13:29:29: #2 predicted fragment length is 116 bps INFO @ Tue, 02 Aug 2022 13:29:29: #2 alternative fragment length(s) may be 116 bps INFO @ Tue, 02 Aug 2022 13:29:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.05_model.r WARNING @ Tue, 02 Aug 2022 13:29:29: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:29:29: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Tue, 02 Aug 2022 13:29:29: #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 13:29:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:29:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:29:32: 11000000 INFO @ Tue, 02 Aug 2022 13:29:33: 5000000 INFO @ Tue, 02 Aug 2022 13:29:38: 12000000 INFO @ Tue, 02 Aug 2022 13:29:39: 6000000 INFO @ Tue, 02 Aug 2022 13:29:44: 13000000 INFO @ Tue, 02 Aug 2022 13:29:45: 7000000 INFO @ Tue, 02 Aug 2022 13:29:50: 14000000 INFO @ Tue, 02 Aug 2022 13:29:51: 8000000 INFO @ Tue, 02 Aug 2022 13:29:52: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:29:52: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:29:52: #1 total tags in treatment: 14211846 INFO @ Tue, 02 Aug 2022 13:29:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:29:52: #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 13:29:52: #1 tags after filtering in treatment: 14211846 INFO @ Tue, 02 Aug 2022 13:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:29:52: #1 finished! INFO @ Tue, 02 Aug 2022 13:29:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:29:53: #2 number of paired peaks: 118 WARNING @ Tue, 02 Aug 2022 13:29:53: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 02 Aug 2022 13:29:53: start model_add_line... INFO @ Tue, 02 Aug 2022 13:29:53: start X-correlation... INFO @ Tue, 02 Aug 2022 13:29:53: end of X-cor INFO @ Tue, 02 Aug 2022 13:29:53: #2 finished! INFO @ Tue, 02 Aug 2022 13:29:53: #2 predicted fragment length is 116 bps INFO @ Tue, 02 Aug 2022 13:29:53: #2 alternative fragment length(s) may be 116 bps INFO @ Tue, 02 Aug 2022 13:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.10_model.r WARNING @ Tue, 02 Aug 2022 13:29:53: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:29:53: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Tue, 02 Aug 2022 13:29:53: #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 13:29:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:29:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:29:57: 9000000 INFO @ Tue, 02 Aug 2022 13:30:03: 10000000 INFO @ Tue, 02 Aug 2022 13:30:09: 11000000 INFO @ Tue, 02 Aug 2022 13:30:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:30:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:30:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.05_summits.bed INFO @ Tue, 02 Aug 2022 13:30:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12531 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:30:15: 12000000 INFO @ Tue, 02 Aug 2022 13:30:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:30:21: 13000000 INFO @ Tue, 02 Aug 2022 13:30:27: 14000000 INFO @ Tue, 02 Aug 2022 13:30:29: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:30:29: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:30:29: #1 total tags in treatment: 14211846 INFO @ Tue, 02 Aug 2022 13:30:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:30:29: #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 13:30:29: #1 tags after filtering in treatment: 14211846 INFO @ Tue, 02 Aug 2022 13:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:30:29: #1 finished! INFO @ Tue, 02 Aug 2022 13:30:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:30:30: #2 number of paired peaks: 118 WARNING @ Tue, 02 Aug 2022 13:30:30: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 02 Aug 2022 13:30:30: start model_add_line... INFO @ Tue, 02 Aug 2022 13:30:30: start X-correlation... INFO @ Tue, 02 Aug 2022 13:30:30: end of X-cor INFO @ Tue, 02 Aug 2022 13:30:30: #2 finished! INFO @ Tue, 02 Aug 2022 13:30:30: #2 predicted fragment length is 116 bps INFO @ Tue, 02 Aug 2022 13:30:30: #2 alternative fragment length(s) may be 116 bps INFO @ Tue, 02 Aug 2022 13:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.20_model.r WARNING @ Tue, 02 Aug 2022 13:30:30: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:30:30: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Tue, 02 Aug 2022 13:30:30: #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 13:30:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:30:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:30:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:30:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.10_summits.bed INFO @ Tue, 02 Aug 2022 13:30:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5902 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:30:56: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:31:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:31:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261322/SRX12261322.20_summits.bed INFO @ Tue, 02 Aug 2022 13:31:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1682 records, 4 fields): 47 millis CompletedMACS2peakCalling BigWig に変換しました。