Job ID = 16437938 SRX = SRX14148450 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21712479 spots for SRR17992821/SRR17992821.sra Written 21712479 spots for SRR17992821/SRR17992821.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438067 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:56 21712479 reads; of these: 21712479 (100.00%) were unpaired; of these: 934875 (4.31%) aligned 0 times 14279674 (65.77%) aligned exactly 1 time 6497930 (29.93%) aligned >1 times 95.69% overall alignment rate Time searching: 00:08:57 Overall time: 00:08:57 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] 2809714 / 20777604 = 0.1352 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 13:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.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 13:29:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:29:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:29:11: 1000000 INFO @ Tue, 02 Aug 2022 13:29:17: 2000000 INFO @ Tue, 02 Aug 2022 13:29:23: 3000000 INFO @ Tue, 02 Aug 2022 13:29:29: 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 13:29:34: 5000000 INFO @ Tue, 02 Aug 2022 13:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.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 13:29:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:29:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:29:41: 6000000 INFO @ Tue, 02 Aug 2022 13:29:41: 1000000 INFO @ Tue, 02 Aug 2022 13:29:47: 7000000 INFO @ Tue, 02 Aug 2022 13:29:48: 2000000 INFO @ Tue, 02 Aug 2022 13:29:54: 8000000 INFO @ Tue, 02 Aug 2022 13:29:54: 3000000 INFO @ Tue, 02 Aug 2022 13:30:01: 9000000 INFO @ Tue, 02 Aug 2022 13:30:01: 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 13:30:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.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 13:30:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:30:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:30:08: 10000000 INFO @ Tue, 02 Aug 2022 13:30:08: 5000000 INFO @ Tue, 02 Aug 2022 13:30:11: 1000000 INFO @ Tue, 02 Aug 2022 13:30:14: 11000000 INFO @ Tue, 02 Aug 2022 13:30:15: 6000000 INFO @ Tue, 02 Aug 2022 13:30:18: 2000000 INFO @ Tue, 02 Aug 2022 13:30:22: 7000000 INFO @ Tue, 02 Aug 2022 13:30:22: 12000000 INFO @ Tue, 02 Aug 2022 13:30:25: 3000000 INFO @ Tue, 02 Aug 2022 13:30:28: 8000000 INFO @ Tue, 02 Aug 2022 13:30:29: 13000000 INFO @ Tue, 02 Aug 2022 13:30:31: 4000000 INFO @ Tue, 02 Aug 2022 13:30:35: 9000000 INFO @ Tue, 02 Aug 2022 13:30:36: 14000000 INFO @ Tue, 02 Aug 2022 13:30:38: 5000000 INFO @ Tue, 02 Aug 2022 13:30:41: 10000000 INFO @ Tue, 02 Aug 2022 13:30:43: 15000000 INFO @ Tue, 02 Aug 2022 13:30:44: 6000000 INFO @ Tue, 02 Aug 2022 13:30:48: 11000000 INFO @ Tue, 02 Aug 2022 13:30:49: 16000000 INFO @ Tue, 02 Aug 2022 13:30:51: 7000000 INFO @ Tue, 02 Aug 2022 13:30:55: 12000000 INFO @ Tue, 02 Aug 2022 13:30:57: 17000000 INFO @ Tue, 02 Aug 2022 13:30:57: 8000000 INFO @ Tue, 02 Aug 2022 13:31:01: 13000000 INFO @ Tue, 02 Aug 2022 13:31:03: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:31:03: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:31:03: #1 total tags in treatment: 17967890 INFO @ Tue, 02 Aug 2022 13:31:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:31:03: #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 13:31:04: #1 tags after filtering in treatment: 17967890 INFO @ Tue, 02 Aug 2022 13:31:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:31:04: #1 finished! INFO @ Tue, 02 Aug 2022 13:31:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:31:04: 9000000 INFO @ Tue, 02 Aug 2022 13:31:05: #2 number of paired peaks: 692 WARNING @ Tue, 02 Aug 2022 13:31:05: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 02 Aug 2022 13:31:05: start model_add_line... INFO @ Tue, 02 Aug 2022 13:31:05: start X-correlation... INFO @ Tue, 02 Aug 2022 13:31:05: end of X-cor INFO @ Tue, 02 Aug 2022 13:31:05: #2 finished! INFO @ Tue, 02 Aug 2022 13:31:05: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 13:31:05: #2 alternative fragment length(s) may be 4,86,576,597 bps INFO @ Tue, 02 Aug 2022 13:31:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.05_model.r WARNING @ Tue, 02 Aug 2022 13:31:05: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:31:05: #2 You may need to consider one of the other alternative d(s): 4,86,576,597 WARNING @ Tue, 02 Aug 2022 13:31:05: #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 13:31:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:31:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:31:08: 14000000 INFO @ Tue, 02 Aug 2022 13:31:11: 10000000 INFO @ Tue, 02 Aug 2022 13:31:15: 15000000 INFO @ Tue, 02 Aug 2022 13:31:17: 11000000 INFO @ Tue, 02 Aug 2022 13:31:21: 16000000 INFO @ Tue, 02 Aug 2022 13:31:24: 12000000 INFO @ Tue, 02 Aug 2022 13:31:28: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:31:30: 13000000 INFO @ Tue, 02 Aug 2022 13:31:35: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:31:35: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:31:35: #1 total tags in treatment: 17967890 INFO @ Tue, 02 Aug 2022 13:31:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:31:35: #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 13:31:35: #1 tags after filtering in treatment: 17967890 INFO @ Tue, 02 Aug 2022 13:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:31:35: #1 finished! INFO @ Tue, 02 Aug 2022 13:31:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:31:36: #2 number of paired peaks: 692 WARNING @ Tue, 02 Aug 2022 13:31:36: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 02 Aug 2022 13:31:36: start model_add_line... INFO @ Tue, 02 Aug 2022 13:31:36: start X-correlation... INFO @ Tue, 02 Aug 2022 13:31:36: end of X-cor INFO @ Tue, 02 Aug 2022 13:31:36: #2 finished! INFO @ Tue, 02 Aug 2022 13:31:36: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 13:31:36: #2 alternative fragment length(s) may be 4,86,576,597 bps INFO @ Tue, 02 Aug 2022 13:31:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.10_model.r WARNING @ Tue, 02 Aug 2022 13:31:36: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:31:36: #2 You may need to consider one of the other alternative d(s): 4,86,576,597 WARNING @ Tue, 02 Aug 2022 13:31:36: #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 13:31:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:31:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:31:37: 14000000 INFO @ Tue, 02 Aug 2022 13:31:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:31:43: 15000000 INFO @ Tue, 02 Aug 2022 13:31:49: 16000000 INFO @ Tue, 02 Aug 2022 13:31:56: 17000000 INFO @ Tue, 02 Aug 2022 13:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.05_summits.bed INFO @ Tue, 02 Aug 2022 13:31:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3093 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:32:02: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:32:02: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:32:02: #1 total tags in treatment: 17967890 INFO @ Tue, 02 Aug 2022 13:32:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:32:02: #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 13:32:02: #1 tags after filtering in treatment: 17967890 INFO @ Tue, 02 Aug 2022 13:32:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:32:02: #1 finished! INFO @ Tue, 02 Aug 2022 13:32:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:32:03: #2 number of paired peaks: 692 WARNING @ Tue, 02 Aug 2022 13:32:03: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 02 Aug 2022 13:32:03: start model_add_line... INFO @ Tue, 02 Aug 2022 13:32:03: start X-correlation... INFO @ Tue, 02 Aug 2022 13:32:03: end of X-cor INFO @ Tue, 02 Aug 2022 13:32:03: #2 finished! INFO @ Tue, 02 Aug 2022 13:32:03: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 13:32:03: #2 alternative fragment length(s) may be 4,86,576,597 bps INFO @ Tue, 02 Aug 2022 13:32:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.20_model.r WARNING @ Tue, 02 Aug 2022 13:32:03: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:32:03: #2 You may need to consider one of the other alternative d(s): 4,86,576,597 WARNING @ Tue, 02 Aug 2022 13:32:03: #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 13:32:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:32:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:32:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:32:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:32:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:32:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.10_summits.bed INFO @ Tue, 02 Aug 2022 13:32:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1756 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:32:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148450/SRX14148450.20_summits.bed INFO @ Tue, 02 Aug 2022 13:32:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (965 records, 4 fields): 91 millis CompletedMACS2peakCalling