Job ID = 16437780 SRX = SRX12261329 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21432070 spots for SRR15972585/SRR15972585.sra Written 21432070 spots for SRR15972585/SRR15972585.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438068 ("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: 00:14:35 21432070 reads; of these: 21432070 (100.00%) were unpaired; of these: 663921 (3.10%) aligned 0 times 12921677 (60.29%) aligned exactly 1 time 7846472 (36.61%) aligned >1 times 96.90% overall alignment rate Time searching: 00:14:35 Overall time: 00:14:35 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] 6829972 / 20768149 = 0.3289 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 13:29:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.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 13:29:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:29:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:30:04: 1000000 INFO @ Tue, 02 Aug 2022 13:30:11: 2000000 INFO @ Tue, 02 Aug 2022 13:30:17: 3000000 INFO @ Tue, 02 Aug 2022 13:30:23: 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 13:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.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 13:30:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:30:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:30:30: 5000000 INFO @ Tue, 02 Aug 2022 13:30:36: 1000000 INFO @ Tue, 02 Aug 2022 13:30:36: 6000000 INFO @ Tue, 02 Aug 2022 13:30:43: 7000000 INFO @ Tue, 02 Aug 2022 13:30:44: 2000000 INFO @ Tue, 02 Aug 2022 13:30:49: 8000000 INFO @ Tue, 02 Aug 2022 13:30:52: 3000000 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 13:30:56: 9000000 INFO @ Tue, 02 Aug 2022 13:30:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.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 13:30:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:30:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:31:00: 4000000 INFO @ Tue, 02 Aug 2022 13:31:02: 10000000 INFO @ Tue, 02 Aug 2022 13:31:06: 1000000 INFO @ Tue, 02 Aug 2022 13:31:08: 5000000 INFO @ Tue, 02 Aug 2022 13:31:09: 11000000 INFO @ Tue, 02 Aug 2022 13:31:14: 2000000 INFO @ Tue, 02 Aug 2022 13:31:15: 6000000 INFO @ Tue, 02 Aug 2022 13:31:16: 12000000 INFO @ Tue, 02 Aug 2022 13:31:22: 13000000 INFO @ Tue, 02 Aug 2022 13:31:22: 3000000 INFO @ Tue, 02 Aug 2022 13:31:23: 7000000 INFO @ Tue, 02 Aug 2022 13:31:28: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:31:28: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:31:28: #1 total tags in treatment: 13938177 INFO @ Tue, 02 Aug 2022 13:31:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:31:28: #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 13:31:28: #1 tags after filtering in treatment: 13938177 INFO @ Tue, 02 Aug 2022 13:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:31:28: #1 finished! INFO @ Tue, 02 Aug 2022 13:31:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:31:29: #2 number of paired peaks: 127 WARNING @ Tue, 02 Aug 2022 13:31:29: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 02 Aug 2022 13:31:29: start model_add_line... INFO @ Tue, 02 Aug 2022 13:31:29: start X-correlation... INFO @ Tue, 02 Aug 2022 13:31:29: end of X-cor INFO @ Tue, 02 Aug 2022 13:31:29: #2 finished! INFO @ Tue, 02 Aug 2022 13:31:29: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 13:31:29: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 02 Aug 2022 13:31:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.05_model.r WARNING @ Tue, 02 Aug 2022 13:31:29: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:31:29: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 02 Aug 2022 13:31:29: #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 13:31:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:31:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:31:30: 4000000 INFO @ Tue, 02 Aug 2022 13:31:32: 8000000 INFO @ Tue, 02 Aug 2022 13:31:38: 5000000 INFO @ Tue, 02 Aug 2022 13:31:40: 9000000 INFO @ Tue, 02 Aug 2022 13:31:46: 6000000 INFO @ Tue, 02 Aug 2022 13:31:48: 10000000 INFO @ Tue, 02 Aug 2022 13:31:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:31:54: 7000000 INFO @ Tue, 02 Aug 2022 13:31:56: 11000000 INFO @ Tue, 02 Aug 2022 13:32:01: 8000000 INFO @ Tue, 02 Aug 2022 13:32:04: 12000000 INFO @ Tue, 02 Aug 2022 13:32:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:32:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:32:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.05_summits.bed INFO @ Tue, 02 Aug 2022 13:32:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4383 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:32:09: 9000000 INFO @ Tue, 02 Aug 2022 13:32:13: 13000000 INFO @ Tue, 02 Aug 2022 13:32:17: 10000000 INFO @ Tue, 02 Aug 2022 13:32:20: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:32:20: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:32:20: #1 total tags in treatment: 13938177 INFO @ Tue, 02 Aug 2022 13:32:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:32:20: #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 13:32:21: #1 tags after filtering in treatment: 13938177 INFO @ Tue, 02 Aug 2022 13:32:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:32:21: #1 finished! INFO @ Tue, 02 Aug 2022 13:32:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:32:22: #2 number of paired peaks: 127 WARNING @ Tue, 02 Aug 2022 13:32:22: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 02 Aug 2022 13:32:22: start model_add_line... INFO @ Tue, 02 Aug 2022 13:32:22: start X-correlation... INFO @ Tue, 02 Aug 2022 13:32:22: end of X-cor INFO @ Tue, 02 Aug 2022 13:32:22: #2 finished! INFO @ Tue, 02 Aug 2022 13:32:22: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 13:32:22: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 02 Aug 2022 13:32:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.10_model.r WARNING @ Tue, 02 Aug 2022 13:32:22: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:32:22: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 02 Aug 2022 13:32:22: #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 13:32:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:32:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:32:24: 11000000 INFO @ Tue, 02 Aug 2022 13:32:32: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:32:39: 13000000 INFO @ Tue, 02 Aug 2022 13:32:46: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:32:46: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:32:46: #1 total tags in treatment: 13938177 INFO @ Tue, 02 Aug 2022 13:32:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:32:46: #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 13:32:47: #1 tags after filtering in treatment: 13938177 INFO @ Tue, 02 Aug 2022 13:32:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:32:47: #1 finished! INFO @ Tue, 02 Aug 2022 13:32:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:32:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:32:48: #2 number of paired peaks: 127 WARNING @ Tue, 02 Aug 2022 13:32:48: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 02 Aug 2022 13:32:48: start model_add_line... INFO @ Tue, 02 Aug 2022 13:32:48: start X-correlation... INFO @ Tue, 02 Aug 2022 13:32:48: end of X-cor INFO @ Tue, 02 Aug 2022 13:32:48: #2 finished! INFO @ Tue, 02 Aug 2022 13:32:48: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 13:32:48: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 02 Aug 2022 13:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.20_model.r WARNING @ Tue, 02 Aug 2022 13:32:48: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:32:48: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 02 Aug 2022 13:32:48: #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 13:32:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:32:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.10_summits.bed INFO @ Tue, 02 Aug 2022 13:33:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1668 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:33:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:33:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:33:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:33:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261329/SRX12261329.20_summits.bed INFO @ Tue, 02 Aug 2022 13:33:25: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (683 records, 4 fields): 48 millis CompletedMACS2peakCalling