Job ID = 10165859 SRX = SRX7723700 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32219639 spots for SRR11084656/SRR11084656.sra Written 32219639 spots for SRR11084656/SRR11084656.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166272 ("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: 00:15:05 32219639 reads; of these: 32219639 (100.00%) were unpaired; of these: 8239876 (25.57%) aligned 0 times 15554481 (48.28%) aligned exactly 1 time 8425282 (26.15%) aligned >1 times 74.43% overall alignment rate Time searching: 00:15:05 Overall time: 00:15:05 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] 6459670 / 23979763 = 0.2694 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 @ Thu, 08 Oct 2020 20:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.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 @ Thu, 08 Oct 2020 20:25:02: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:25:02: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:25:10: 1000000 INFO @ Thu, 08 Oct 2020 20:25:18: 2000000 INFO @ Thu, 08 Oct 2020 20:25:26: 3000000 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 @ Thu, 08 Oct 2020 20:25:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.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 @ Thu, 08 Oct 2020 20:25:32: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:25:32: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:25:34: 4000000 INFO @ Thu, 08 Oct 2020 20:25:41: 1000000 INFO @ Thu, 08 Oct 2020 20:25:43: 5000000 INFO @ Thu, 08 Oct 2020 20:25:49: 2000000 INFO @ Thu, 08 Oct 2020 20:25:52: 6000000 INFO @ Thu, 08 Oct 2020 20:25:58: 3000000 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 @ Thu, 08 Oct 2020 20:26:01: 7000000 INFO @ Thu, 08 Oct 2020 20:26:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.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 @ Thu, 08 Oct 2020 20:26:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:26:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:26:07: 4000000 INFO @ Thu, 08 Oct 2020 20:26:10: 8000000 INFO @ Thu, 08 Oct 2020 20:26:13: 1000000 INFO @ Thu, 08 Oct 2020 20:26:16: 5000000 INFO @ Thu, 08 Oct 2020 20:26:19: 9000000 INFO @ Thu, 08 Oct 2020 20:26:22: 2000000 INFO @ Thu, 08 Oct 2020 20:26:25: 6000000 INFO @ Thu, 08 Oct 2020 20:26:28: 10000000 INFO @ Thu, 08 Oct 2020 20:26:31: 3000000 INFO @ Thu, 08 Oct 2020 20:26:34: 7000000 INFO @ Thu, 08 Oct 2020 20:26:37: 11000000 INFO @ Thu, 08 Oct 2020 20:26:40: 4000000 INFO @ Thu, 08 Oct 2020 20:26:43: 8000000 INFO @ Thu, 08 Oct 2020 20:26:46: 12000000 INFO @ Thu, 08 Oct 2020 20:26:49: 5000000 INFO @ Thu, 08 Oct 2020 20:26:52: 9000000 INFO @ Thu, 08 Oct 2020 20:26:55: 13000000 INFO @ Thu, 08 Oct 2020 20:26:58: 6000000 INFO @ Thu, 08 Oct 2020 20:27:01: 10000000 INFO @ Thu, 08 Oct 2020 20:27:04: 14000000 INFO @ Thu, 08 Oct 2020 20:27:07: 7000000 INFO @ Thu, 08 Oct 2020 20:27:11: 11000000 INFO @ Thu, 08 Oct 2020 20:27:13: 15000000 INFO @ Thu, 08 Oct 2020 20:27:16: 8000000 INFO @ Thu, 08 Oct 2020 20:27:20: 12000000 INFO @ Thu, 08 Oct 2020 20:27:22: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:27:26: 9000000 INFO @ Thu, 08 Oct 2020 20:27:29: 13000000 INFO @ Thu, 08 Oct 2020 20:27:31: 17000000 INFO @ Thu, 08 Oct 2020 20:27:35: 10000000 INFO @ Thu, 08 Oct 2020 20:27:35: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:27:35: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:27:35: #1 total tags in treatment: 17520093 INFO @ Thu, 08 Oct 2020 20:27:35: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:27:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:27:35: #1 tags after filtering in treatment: 17520093 INFO @ Thu, 08 Oct 2020 20:27:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:27:35: #1 finished! INFO @ Thu, 08 Oct 2020 20:27:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:27:36: #2 number of paired peaks: 137 WARNING @ Thu, 08 Oct 2020 20:27:36: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Thu, 08 Oct 2020 20:27:36: start model_add_line... INFO @ Thu, 08 Oct 2020 20:27:37: start X-correlation... INFO @ Thu, 08 Oct 2020 20:27:37: end of X-cor INFO @ Thu, 08 Oct 2020 20:27:37: #2 finished! INFO @ Thu, 08 Oct 2020 20:27:37: #2 predicted fragment length is 38 bps INFO @ Thu, 08 Oct 2020 20:27:37: #2 alternative fragment length(s) may be 38 bps INFO @ Thu, 08 Oct 2020 20:27:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05_model.r WARNING @ Thu, 08 Oct 2020 20:27:37: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:27:37: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Thu, 08 Oct 2020 20:27:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:27:37: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:27:38: 14000000 INFO @ Thu, 08 Oct 2020 20:27:44: 11000000 INFO @ Thu, 08 Oct 2020 20:27:47: 15000000 INFO @ Thu, 08 Oct 2020 20:27:53: 12000000 INFO @ Thu, 08 Oct 2020 20:27:56: 16000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:28:02: 13000000 INFO @ Thu, 08 Oct 2020 20:28:04: 17000000 INFO @ Thu, 08 Oct 2020 20:28:09: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:28:09: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:28:09: #1 total tags in treatment: 17520093 INFO @ Thu, 08 Oct 2020 20:28:09: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:28:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:28:09: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:28:09: #1 tags after filtering in treatment: 17520093 INFO @ Thu, 08 Oct 2020 20:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:28:09: #1 finished! INFO @ Thu, 08 Oct 2020 20:28:09: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:28:10: #2 number of paired peaks: 137 WARNING @ Thu, 08 Oct 2020 20:28:10: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Thu, 08 Oct 2020 20:28:10: start model_add_line... INFO @ Thu, 08 Oct 2020 20:28:10: 14000000 INFO @ Thu, 08 Oct 2020 20:28:10: start X-correlation... INFO @ Thu, 08 Oct 2020 20:28:10: end of X-cor INFO @ Thu, 08 Oct 2020 20:28:10: #2 finished! INFO @ Thu, 08 Oct 2020 20:28:10: #2 predicted fragment length is 38 bps INFO @ Thu, 08 Oct 2020 20:28:10: #2 alternative fragment length(s) may be 38 bps INFO @ Thu, 08 Oct 2020 20:28:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10_model.r WARNING @ Thu, 08 Oct 2020 20:28:10: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:28:10: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Thu, 08 Oct 2020 20:28:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:28:10: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:28:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:28:18: 15000000 INFO @ Thu, 08 Oct 2020 20:28:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:28:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:28:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05_summits.bed INFO @ Thu, 08 Oct 2020 20:28:25: Done! INFO @ Thu, 08 Oct 2020 20:28:26: 16000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6181 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:28:33: 17000000 INFO @ Thu, 08 Oct 2020 20:28:37: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:28:37: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:28:37: #1 total tags in treatment: 17520093 INFO @ Thu, 08 Oct 2020 20:28:37: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:28:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:28:38: #1 tags after filtering in treatment: 17520093 INFO @ Thu, 08 Oct 2020 20:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:28:38: #1 finished! INFO @ Thu, 08 Oct 2020 20:28:38: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:28:39: #2 number of paired peaks: 137 WARNING @ Thu, 08 Oct 2020 20:28:39: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Thu, 08 Oct 2020 20:28:39: start model_add_line... INFO @ Thu, 08 Oct 2020 20:28:39: start X-correlation... INFO @ Thu, 08 Oct 2020 20:28:39: end of X-cor INFO @ Thu, 08 Oct 2020 20:28:39: #2 finished! INFO @ Thu, 08 Oct 2020 20:28:39: #2 predicted fragment length is 38 bps INFO @ Thu, 08 Oct 2020 20:28:39: #2 alternative fragment length(s) may be 38 bps INFO @ Thu, 08 Oct 2020 20:28:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20_model.r WARNING @ Thu, 08 Oct 2020 20:28:39: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:28:39: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Thu, 08 Oct 2020 20:28:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:28:39: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:28:43: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:28:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10_summits.bed INFO @ Thu, 08 Oct 2020 20:28:59: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (2102 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:29:12: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:29:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:29:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:29:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20_summits.bed INFO @ Thu, 08 Oct 2020 20:29:27: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (298 records, 4 fields): 2 millis CompletedMACS2peakCalling