Job ID = 14170548 SRX = SRX9720884 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12540682 spots for SRR13291874/SRR13291874.sra Written 12540682 spots for SRR13291874/SRR13291874.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170952 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:11 12540682 reads; of these: 12540682 (100.00%) were unpaired; of these: 653414 (5.21%) aligned 0 times 7660150 (61.08%) aligned exactly 1 time 4227118 (33.71%) aligned >1 times 94.79% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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 8 files... [bam_rmdupse_core] 1183272 / 11887268 = 0.0995 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:18:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.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 @ Sat, 11 Dec 2021 07:18:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:18:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:18:08: 1000000 INFO @ Sat, 11 Dec 2021 07:18:15: 2000000 INFO @ Sat, 11 Dec 2021 07:18:21: 3000000 INFO @ Sat, 11 Dec 2021 07:18:28: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.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 @ Sat, 11 Dec 2021 07:18:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:18:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:18:35: 5000000 INFO @ Sat, 11 Dec 2021 07:18:38: 1000000 INFO @ Sat, 11 Dec 2021 07:18:42: 6000000 INFO @ Sat, 11 Dec 2021 07:18:44: 2000000 INFO @ Sat, 11 Dec 2021 07:18:49: 7000000 INFO @ Sat, 11 Dec 2021 07:18:51: 3000000 INFO @ Sat, 11 Dec 2021 07:18:56: 8000000 INFO @ Sat, 11 Dec 2021 07:18:58: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.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 @ Sat, 11 Dec 2021 07:19:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:19:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:19:03: 9000000 INFO @ Sat, 11 Dec 2021 07:19:04: 5000000 INFO @ Sat, 11 Dec 2021 07:19:08: 1000000 INFO @ Sat, 11 Dec 2021 07:19:11: 10000000 INFO @ Sat, 11 Dec 2021 07:19:11: 6000000 INFO @ Sat, 11 Dec 2021 07:19:14: 2000000 INFO @ Sat, 11 Dec 2021 07:19:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:19:16: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:19:16: #1 total tags in treatment: 10703996 INFO @ Sat, 11 Dec 2021 07:19:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:19:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:19:16: #1 tags after filtering in treatment: 10703996 INFO @ Sat, 11 Dec 2021 07:19:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:19:16: #1 finished! INFO @ Sat, 11 Dec 2021 07:19:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:19:17: #2 number of paired peaks: 662 WARNING @ Sat, 11 Dec 2021 07:19:17: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Sat, 11 Dec 2021 07:19:17: start model_add_line... INFO @ Sat, 11 Dec 2021 07:19:17: start X-correlation... INFO @ Sat, 11 Dec 2021 07:19:17: end of X-cor INFO @ Sat, 11 Dec 2021 07:19:17: #2 finished! INFO @ Sat, 11 Dec 2021 07:19:17: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 07:19:17: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sat, 11 Dec 2021 07:19:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.05_model.r WARNING @ Sat, 11 Dec 2021 07:19:17: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:19:17: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sat, 11 Dec 2021 07:19:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:19:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:19:17: 7000000 INFO @ Sat, 11 Dec 2021 07:19:21: 3000000 INFO @ Sat, 11 Dec 2021 07:19:24: 8000000 INFO @ Sat, 11 Dec 2021 07:19:27: 4000000 INFO @ Sat, 11 Dec 2021 07:19:30: 9000000 INFO @ Sat, 11 Dec 2021 07:19:34: 5000000 INFO @ Sat, 11 Dec 2021 07:19:37: 10000000 INFO @ Sat, 11 Dec 2021 07:19:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:19:40: 6000000 INFO @ Sat, 11 Dec 2021 07:19:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:19:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:19:41: #1 total tags in treatment: 10703996 INFO @ Sat, 11 Dec 2021 07:19:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:19:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:19:41: #1 tags after filtering in treatment: 10703996 INFO @ Sat, 11 Dec 2021 07:19:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:19:41: #1 finished! INFO @ Sat, 11 Dec 2021 07:19:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:19:42: #2 number of paired peaks: 662 WARNING @ Sat, 11 Dec 2021 07:19:42: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Sat, 11 Dec 2021 07:19:42: start model_add_line... INFO @ Sat, 11 Dec 2021 07:19:42: start X-correlation... INFO @ Sat, 11 Dec 2021 07:19:42: end of X-cor INFO @ Sat, 11 Dec 2021 07:19:42: #2 finished! INFO @ Sat, 11 Dec 2021 07:19:42: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 07:19:42: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sat, 11 Dec 2021 07:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.10_model.r WARNING @ Sat, 11 Dec 2021 07:19:42: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:19:42: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sat, 11 Dec 2021 07:19:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:19:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:19:46: 7000000 INFO @ Sat, 11 Dec 2021 07:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.05_summits.bed INFO @ Sat, 11 Dec 2021 07:19:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2951 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:19:51: 8000000 INFO @ Sat, 11 Dec 2021 07:19:57: 9000000 INFO @ Sat, 11 Dec 2021 07:20:02: 10000000 INFO @ Sat, 11 Dec 2021 07:20:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:20:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:20:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:20:06: #1 total tags in treatment: 10703996 INFO @ Sat, 11 Dec 2021 07:20:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:20:06: #1 tags after filtering in treatment: 10703996 INFO @ Sat, 11 Dec 2021 07:20:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:20:06: #1 finished! INFO @ Sat, 11 Dec 2021 07:20:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:20:07: #2 number of paired peaks: 662 WARNING @ Sat, 11 Dec 2021 07:20:07: Fewer paired peaks (662) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 662 pairs to build model! INFO @ Sat, 11 Dec 2021 07:20:07: start model_add_line... INFO @ Sat, 11 Dec 2021 07:20:07: start X-correlation... INFO @ Sat, 11 Dec 2021 07:20:07: end of X-cor INFO @ Sat, 11 Dec 2021 07:20:07: #2 finished! INFO @ Sat, 11 Dec 2021 07:20:07: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 07:20:07: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sat, 11 Dec 2021 07:20:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.20_model.r WARNING @ Sat, 11 Dec 2021 07:20:07: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:20:07: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sat, 11 Dec 2021 07:20:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:20:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:20:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.10_summits.bed INFO @ Sat, 11 Dec 2021 07:20:14: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1863 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:20:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:20:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:20:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:20:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720884/SRX9720884.20_summits.bed INFO @ Sat, 11 Dec 2021 07:20:39: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 2 millis CompletedMACS2peakCalling