Job ID = 6626638 SRX = SRX7351001 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27964107 spots for SRR10673631/SRR10673631.sra Written 27964107 spots for SRR10673631/SRR10673631.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626830 ("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: 00:12:29 27964107 reads; of these: 27964107 (100.00%) were unpaired; of these: 781186 (2.79%) aligned 0 times 18317331 (65.50%) aligned exactly 1 time 8865590 (31.70%) aligned >1 times 97.21% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 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] 4474176 / 27182921 = 0.1646 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:25:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.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, 14 Jul 2020 08:25:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:25:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:25:50: 1000000 INFO @ Tue, 14 Jul 2020 08:25:56: 2000000 INFO @ Tue, 14 Jul 2020 08:26:02: 3000000 INFO @ Tue, 14 Jul 2020 08:26:08: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:26:14: 5000000 INFO @ Tue, 14 Jul 2020 08:26:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.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, 14 Jul 2020 08:26:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:26:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:26:20: 1000000 INFO @ Tue, 14 Jul 2020 08:26:20: 6000000 INFO @ Tue, 14 Jul 2020 08:26:25: 2000000 INFO @ Tue, 14 Jul 2020 08:26:26: 7000000 INFO @ Tue, 14 Jul 2020 08:26:31: 3000000 INFO @ Tue, 14 Jul 2020 08:26:32: 8000000 INFO @ Tue, 14 Jul 2020 08:26:37: 4000000 INFO @ Tue, 14 Jul 2020 08:26:38: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:26:43: 5000000 INFO @ Tue, 14 Jul 2020 08:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.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, 14 Jul 2020 08:26:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:26:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:26:44: 10000000 INFO @ Tue, 14 Jul 2020 08:26:49: 6000000 INFO @ Tue, 14 Jul 2020 08:26:50: 11000000 INFO @ Tue, 14 Jul 2020 08:26:52: 1000000 INFO @ Tue, 14 Jul 2020 08:26:55: 7000000 INFO @ Tue, 14 Jul 2020 08:26:57: 12000000 INFO @ Tue, 14 Jul 2020 08:26:59: 2000000 INFO @ Tue, 14 Jul 2020 08:27:00: 8000000 INFO @ Tue, 14 Jul 2020 08:27:03: 13000000 INFO @ Tue, 14 Jul 2020 08:27:05: 3000000 INFO @ Tue, 14 Jul 2020 08:27:06: 9000000 INFO @ Tue, 14 Jul 2020 08:27:09: 14000000 INFO @ Tue, 14 Jul 2020 08:27:11: 4000000 INFO @ Tue, 14 Jul 2020 08:27:12: 10000000 INFO @ Tue, 14 Jul 2020 08:27:15: 15000000 INFO @ Tue, 14 Jul 2020 08:27:16: 5000000 INFO @ Tue, 14 Jul 2020 08:27:18: 11000000 INFO @ Tue, 14 Jul 2020 08:27:21: 16000000 INFO @ Tue, 14 Jul 2020 08:27:22: 6000000 INFO @ Tue, 14 Jul 2020 08:27:24: 12000000 INFO @ Tue, 14 Jul 2020 08:27:27: 17000000 INFO @ Tue, 14 Jul 2020 08:27:28: 7000000 INFO @ Tue, 14 Jul 2020 08:27:29: 13000000 INFO @ Tue, 14 Jul 2020 08:27:33: 18000000 INFO @ Tue, 14 Jul 2020 08:27:34: 8000000 INFO @ Tue, 14 Jul 2020 08:27:35: 14000000 INFO @ Tue, 14 Jul 2020 08:27:39: 9000000 INFO @ Tue, 14 Jul 2020 08:27:39: 19000000 INFO @ Tue, 14 Jul 2020 08:27:41: 15000000 INFO @ Tue, 14 Jul 2020 08:27:45: 10000000 INFO @ Tue, 14 Jul 2020 08:27:45: 20000000 INFO @ Tue, 14 Jul 2020 08:27:47: 16000000 INFO @ Tue, 14 Jul 2020 08:27:51: 11000000 INFO @ Tue, 14 Jul 2020 08:27:52: 21000000 INFO @ Tue, 14 Jul 2020 08:27:52: 17000000 INFO @ Tue, 14 Jul 2020 08:27:56: 12000000 INFO @ Tue, 14 Jul 2020 08:27:58: 22000000 INFO @ Tue, 14 Jul 2020 08:27:58: 18000000 INFO @ Tue, 14 Jul 2020 08:28:02: 13000000 INFO @ Tue, 14 Jul 2020 08:28:02: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:28:02: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:28:02: #1 total tags in treatment: 22708745 INFO @ Tue, 14 Jul 2020 08:28:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:28:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:28:03: #1 tags after filtering in treatment: 22708745 INFO @ Tue, 14 Jul 2020 08:28:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:28:03: #1 finished! INFO @ Tue, 14 Jul 2020 08:28:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:28:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:28:04: 19000000 INFO @ Tue, 14 Jul 2020 08:28:04: #2 number of paired peaks: 547 WARNING @ Tue, 14 Jul 2020 08:28:04: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Tue, 14 Jul 2020 08:28:04: start model_add_line... INFO @ Tue, 14 Jul 2020 08:28:04: start X-correlation... INFO @ Tue, 14 Jul 2020 08:28:04: end of X-cor INFO @ Tue, 14 Jul 2020 08:28:04: #2 finished! INFO @ Tue, 14 Jul 2020 08:28:04: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 08:28:04: #2 alternative fragment length(s) may be 2,64 bps INFO @ Tue, 14 Jul 2020 08:28:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.05_model.r WARNING @ Tue, 14 Jul 2020 08:28:04: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:28:04: #2 You may need to consider one of the other alternative d(s): 2,64 WARNING @ Tue, 14 Jul 2020 08:28:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:28:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:28:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:28:07: 14000000 INFO @ Tue, 14 Jul 2020 08:28:10: 20000000 INFO @ Tue, 14 Jul 2020 08:28:13: 15000000 INFO @ Tue, 14 Jul 2020 08:28:15: 21000000 INFO @ Tue, 14 Jul 2020 08:28:19: 16000000 INFO @ Tue, 14 Jul 2020 08:28:21: 22000000 INFO @ Tue, 14 Jul 2020 08:28:24: 17000000 INFO @ Tue, 14 Jul 2020 08:28:25: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:28:25: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:28:25: #1 total tags in treatment: 22708745 INFO @ Tue, 14 Jul 2020 08:28:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:28:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:28:26: #1 tags after filtering in treatment: 22708745 INFO @ Tue, 14 Jul 2020 08:28:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:28:26: #1 finished! INFO @ Tue, 14 Jul 2020 08:28:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:28:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:28:27: #2 number of paired peaks: 547 WARNING @ Tue, 14 Jul 2020 08:28:27: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Tue, 14 Jul 2020 08:28:27: start model_add_line... INFO @ Tue, 14 Jul 2020 08:28:27: start X-correlation... INFO @ Tue, 14 Jul 2020 08:28:27: end of X-cor INFO @ Tue, 14 Jul 2020 08:28:27: #2 finished! INFO @ Tue, 14 Jul 2020 08:28:27: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 08:28:27: #2 alternative fragment length(s) may be 2,64 bps INFO @ Tue, 14 Jul 2020 08:28:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.10_model.r WARNING @ Tue, 14 Jul 2020 08:28:27: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:28:27: #2 You may need to consider one of the other alternative d(s): 2,64 WARNING @ Tue, 14 Jul 2020 08:28:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:28:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:28:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:28:30: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:28:35: 19000000 INFO @ Tue, 14 Jul 2020 08:28:41: 20000000 INFO @ Tue, 14 Jul 2020 08:28:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:28:46: 21000000 INFO @ Tue, 14 Jul 2020 08:28:52: 22000000 INFO @ Tue, 14 Jul 2020 08:28:56: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:28:56: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:28:56: #1 total tags in treatment: 22708745 INFO @ Tue, 14 Jul 2020 08:28:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:28:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:28:56: #1 tags after filtering in treatment: 22708745 INFO @ Tue, 14 Jul 2020 08:28:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:28:56: #1 finished! INFO @ Tue, 14 Jul 2020 08:28:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:28:57: #2 number of paired peaks: 547 WARNING @ Tue, 14 Jul 2020 08:28:57: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Tue, 14 Jul 2020 08:28:57: start model_add_line... INFO @ Tue, 14 Jul 2020 08:28:58: start X-correlation... INFO @ Tue, 14 Jul 2020 08:28:58: end of X-cor INFO @ Tue, 14 Jul 2020 08:28:58: #2 finished! INFO @ Tue, 14 Jul 2020 08:28:58: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 08:28:58: #2 alternative fragment length(s) may be 2,64 bps INFO @ Tue, 14 Jul 2020 08:28:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.20_model.r WARNING @ Tue, 14 Jul 2020 08:28:58: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:28:58: #2 You may need to consider one of the other alternative d(s): 2,64 WARNING @ Tue, 14 Jul 2020 08:28:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:28:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.05_summits.bed INFO @ Tue, 14 Jul 2020 08:29:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3171 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:29:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:29:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:29:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:29:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.10_summits.bed INFO @ Tue, 14 Jul 2020 08:29:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1875 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:29:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351001/SRX7351001.20_summits.bed INFO @ Tue, 14 Jul 2020 08:30:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (982 records, 4 fields): 19 millis CompletedMACS2peakCalling