Job ID = 14166962 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 14167294 ("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: 00:14:12 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: 00:14:12 Overall time: 00:14:12 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 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:27:56: # 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 @ Fri, 10 Dec 2021 08:27:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:27:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:28:03: 1000000 INFO @ Fri, 10 Dec 2021 08:28:09: 2000000 INFO @ Fri, 10 Dec 2021 08:28:16: 3000000 INFO @ Fri, 10 Dec 2021 08:28:23: 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 @ Fri, 10 Dec 2021 08:28:26: # 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 @ Fri, 10 Dec 2021 08:28:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:28:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:28:30: 5000000 INFO @ Fri, 10 Dec 2021 08:28:34: 1000000 INFO @ Fri, 10 Dec 2021 08:28:38: 6000000 INFO @ Fri, 10 Dec 2021 08:28:42: 2000000 INFO @ Fri, 10 Dec 2021 08:28:46: 7000000 INFO @ Fri, 10 Dec 2021 08:28:50: 3000000 INFO @ Fri, 10 Dec 2021 08:28:53: 8000000 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 @ Fri, 10 Dec 2021 08:28:56: # 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 @ Fri, 10 Dec 2021 08:28:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:28:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:28:58: 4000000 INFO @ Fri, 10 Dec 2021 08:29:02: 9000000 INFO @ Fri, 10 Dec 2021 08:29:06: 1000000 INFO @ Fri, 10 Dec 2021 08:29:06: 5000000 INFO @ Fri, 10 Dec 2021 08:29:10: 10000000 INFO @ Fri, 10 Dec 2021 08:29:15: 6000000 INFO @ Fri, 10 Dec 2021 08:29:15: 2000000 INFO @ Fri, 10 Dec 2021 08:29:19: 11000000 INFO @ Fri, 10 Dec 2021 08:29:23: 7000000 INFO @ Fri, 10 Dec 2021 08:29:25: 3000000 INFO @ Fri, 10 Dec 2021 08:29:27: 12000000 INFO @ Fri, 10 Dec 2021 08:29:32: 8000000 INFO @ Fri, 10 Dec 2021 08:29:35: 4000000 INFO @ Fri, 10 Dec 2021 08:29:35: 13000000 INFO @ Fri, 10 Dec 2021 08:29:41: 9000000 INFO @ Fri, 10 Dec 2021 08:29:44: 14000000 INFO @ Fri, 10 Dec 2021 08:29:44: 5000000 INFO @ Fri, 10 Dec 2021 08:29:50: 10000000 INFO @ Fri, 10 Dec 2021 08:29:52: 15000000 INFO @ Fri, 10 Dec 2021 08:29:54: 6000000 INFO @ Fri, 10 Dec 2021 08:29:58: 11000000 INFO @ Fri, 10 Dec 2021 08:30:01: 16000000 INFO @ Fri, 10 Dec 2021 08:30:03: 7000000 INFO @ Fri, 10 Dec 2021 08:30:07: 12000000 INFO @ Fri, 10 Dec 2021 08:30:09: 17000000 INFO @ Fri, 10 Dec 2021 08:30:12: 8000000 INFO @ Fri, 10 Dec 2021 08:30:14: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:30:14: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:30:14: #1 total tags in treatment: 17520093 INFO @ Fri, 10 Dec 2021 08:30:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:30:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:30:14: #1 tags after filtering in treatment: 17520093 INFO @ Fri, 10 Dec 2021 08:30:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:30:14: #1 finished! INFO @ Fri, 10 Dec 2021 08:30:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:30:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:30:15: #2 number of paired peaks: 137 WARNING @ Fri, 10 Dec 2021 08:30:15: 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 @ Fri, 10 Dec 2021 08:30:15: start model_add_line... INFO @ Fri, 10 Dec 2021 08:30:15: 13000000 INFO @ Fri, 10 Dec 2021 08:30:15: start X-correlation... INFO @ Fri, 10 Dec 2021 08:30:15: end of X-cor INFO @ Fri, 10 Dec 2021 08:30:15: #2 finished! INFO @ Fri, 10 Dec 2021 08:30:15: #2 predicted fragment length is 38 bps INFO @ Fri, 10 Dec 2021 08:30:15: #2 alternative fragment length(s) may be 38 bps INFO @ Fri, 10 Dec 2021 08:30:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05_model.r WARNING @ Fri, 10 Dec 2021 08:30:15: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:30:15: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Fri, 10 Dec 2021 08:30:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:30:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:30:15: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:30:22: 9000000 INFO @ Fri, 10 Dec 2021 08:30:24: 14000000 INFO @ Fri, 10 Dec 2021 08:30:31: 10000000 INFO @ Fri, 10 Dec 2021 08:30:32: 15000000 INFO @ Fri, 10 Dec 2021 08:30:41: 16000000 INFO @ Fri, 10 Dec 2021 08:30:41: 11000000 INFO @ Fri, 10 Dec 2021 08:30:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:30:49: 17000000 INFO @ Fri, 10 Dec 2021 08:30:50: 12000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:30:53: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:30:53: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:30:53: #1 total tags in treatment: 17520093 INFO @ Fri, 10 Dec 2021 08:30:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:30:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:30:54: #1 tags after filtering in treatment: 17520093 INFO @ Fri, 10 Dec 2021 08:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:30:54: #1 finished! INFO @ Fri, 10 Dec 2021 08:30:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:30:55: #2 number of paired peaks: 137 WARNING @ Fri, 10 Dec 2021 08:30:55: 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 @ Fri, 10 Dec 2021 08:30:55: start model_add_line... INFO @ Fri, 10 Dec 2021 08:30:55: start X-correlation... INFO @ Fri, 10 Dec 2021 08:30:55: end of X-cor INFO @ Fri, 10 Dec 2021 08:30:55: #2 finished! INFO @ Fri, 10 Dec 2021 08:30:55: #2 predicted fragment length is 38 bps INFO @ Fri, 10 Dec 2021 08:30:55: #2 alternative fragment length(s) may be 38 bps INFO @ Fri, 10 Dec 2021 08:30:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10_model.r WARNING @ Fri, 10 Dec 2021 08:30:55: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:30:55: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Fri, 10 Dec 2021 08:30:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:30:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:30:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:30:59: 13000000 INFO @ Fri, 10 Dec 2021 08:31:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:31:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.05_summits.bed INFO @ Fri, 10 Dec 2021 08:31:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6181 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:31:07: 14000000 INFO @ Fri, 10 Dec 2021 08:31:15: 15000000 INFO @ Fri, 10 Dec 2021 08:31:24: 16000000 INFO @ Fri, 10 Dec 2021 08:31:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:31:32: 17000000 INFO @ Fri, 10 Dec 2021 08:31:36: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:31:36: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:31:36: #1 total tags in treatment: 17520093 INFO @ Fri, 10 Dec 2021 08:31:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:31:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:31:36: #1 tags after filtering in treatment: 17520093 INFO @ Fri, 10 Dec 2021 08:31:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:31:36: #1 finished! INFO @ Fri, 10 Dec 2021 08:31:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:31:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:31:37: #2 number of paired peaks: 137 WARNING @ Fri, 10 Dec 2021 08:31:37: 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 @ Fri, 10 Dec 2021 08:31:37: start model_add_line... INFO @ Fri, 10 Dec 2021 08:31:37: start X-correlation... INFO @ Fri, 10 Dec 2021 08:31:37: end of X-cor INFO @ Fri, 10 Dec 2021 08:31:37: #2 finished! INFO @ Fri, 10 Dec 2021 08:31:37: #2 predicted fragment length is 38 bps INFO @ Fri, 10 Dec 2021 08:31:37: #2 alternative fragment length(s) may be 38 bps INFO @ Fri, 10 Dec 2021 08:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20_model.r WARNING @ Fri, 10 Dec 2021 08:31:37: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:31:37: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Fri, 10 Dec 2021 08:31:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:31:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:31:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:31:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:31:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.10_summits.bed INFO @ Fri, 10 Dec 2021 08:31:40: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (2102 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:32:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723700/SRX7723700.20_summits.bed INFO @ Fri, 10 Dec 2021 08:32:22: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (298 records, 4 fields): 1 millis CompletedMACS2peakCalling