Job ID = 14167436 SRX = SRX8688947 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20435163 spots for SRR12174178/SRR12174178.sra Written 20435163 spots for SRR12174178/SRR12174178.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168075 ("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: 00:09:23 20435163 reads; of these: 20435163 (100.00%) were unpaired; of these: 4347579 (21.27%) aligned 0 times 11369232 (55.64%) aligned exactly 1 time 4718352 (23.09%) aligned >1 times 78.73% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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] 1711656 / 16087584 = 0.1064 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 12:34:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.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 12:34:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:34:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:34:12: 1000000 INFO @ Fri, 10 Dec 2021 12:34:17: 2000000 INFO @ Fri, 10 Dec 2021 12:34:22: 3000000 INFO @ Fri, 10 Dec 2021 12:34:27: 4000000 INFO @ Fri, 10 Dec 2021 12:34:32: 5000000 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 12:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.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 12:34:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:34:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:34:37: 6000000 INFO @ Fri, 10 Dec 2021 12:34:42: 1000000 INFO @ Fri, 10 Dec 2021 12:34:42: 7000000 INFO @ Fri, 10 Dec 2021 12:34:47: 2000000 INFO @ Fri, 10 Dec 2021 12:34:47: 8000000 INFO @ Fri, 10 Dec 2021 12:34:52: 3000000 INFO @ Fri, 10 Dec 2021 12:34:53: 9000000 INFO @ Fri, 10 Dec 2021 12:34:58: 10000000 INFO @ Fri, 10 Dec 2021 12:34:58: 4000000 INFO @ Fri, 10 Dec 2021 12:35:03: 11000000 INFO @ Fri, 10 Dec 2021 12:35:03: 5000000 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 12:35:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.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 12:35:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:35:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:35:08: 12000000 INFO @ Fri, 10 Dec 2021 12:35:09: 6000000 INFO @ Fri, 10 Dec 2021 12:35:13: 1000000 INFO @ Fri, 10 Dec 2021 12:35:14: 13000000 INFO @ Fri, 10 Dec 2021 12:35:14: 7000000 INFO @ Fri, 10 Dec 2021 12:35:19: 14000000 INFO @ Fri, 10 Dec 2021 12:35:19: 2000000 INFO @ Fri, 10 Dec 2021 12:35:19: 8000000 INFO @ Fri, 10 Dec 2021 12:35:21: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:35:21: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:35:21: #1 total tags in treatment: 14375928 INFO @ Fri, 10 Dec 2021 12:35:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:35:21: #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 12:35:21: #1 tags after filtering in treatment: 14375928 INFO @ Fri, 10 Dec 2021 12:35:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:35:21: #1 finished! INFO @ Fri, 10 Dec 2021 12:35:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:35:22: #2 number of paired peaks: 249 WARNING @ Fri, 10 Dec 2021 12:35:22: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Fri, 10 Dec 2021 12:35:22: start model_add_line... INFO @ Fri, 10 Dec 2021 12:35:22: start X-correlation... INFO @ Fri, 10 Dec 2021 12:35:22: end of X-cor INFO @ Fri, 10 Dec 2021 12:35:22: #2 finished! INFO @ Fri, 10 Dec 2021 12:35:22: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:35:22: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 10 Dec 2021 12:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.05_model.r WARNING @ Fri, 10 Dec 2021 12:35:22: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:35:22: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 10 Dec 2021 12:35:22: #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 12:35:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:35:24: 9000000 INFO @ Fri, 10 Dec 2021 12:35:25: 3000000 INFO @ Fri, 10 Dec 2021 12:35:30: 10000000 INFO @ Fri, 10 Dec 2021 12:35:32: 4000000 INFO @ Fri, 10 Dec 2021 12:35:35: 11000000 INFO @ Fri, 10 Dec 2021 12:35:38: 5000000 INFO @ Fri, 10 Dec 2021 12:35:41: 12000000 INFO @ Fri, 10 Dec 2021 12:35:44: 6000000 INFO @ Fri, 10 Dec 2021 12:35:46: 13000000 INFO @ Fri, 10 Dec 2021 12:35:50: 7000000 INFO @ Fri, 10 Dec 2021 12:35:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:35:51: 14000000 INFO @ Fri, 10 Dec 2021 12:35:54: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:35:54: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:35:54: #1 total tags in treatment: 14375928 INFO @ Fri, 10 Dec 2021 12:35:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:35:54: #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 12:35:54: #1 tags after filtering in treatment: 14375928 INFO @ Fri, 10 Dec 2021 12:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:35:54: #1 finished! INFO @ Fri, 10 Dec 2021 12:35:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:35:55: #2 number of paired peaks: 249 WARNING @ Fri, 10 Dec 2021 12:35:55: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Fri, 10 Dec 2021 12:35:55: start model_add_line... INFO @ Fri, 10 Dec 2021 12:35:55: start X-correlation... INFO @ Fri, 10 Dec 2021 12:35:55: end of X-cor INFO @ Fri, 10 Dec 2021 12:35:55: #2 finished! INFO @ Fri, 10 Dec 2021 12:35:55: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:35:55: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 10 Dec 2021 12:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.10_model.r WARNING @ Fri, 10 Dec 2021 12:35:55: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:35:55: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 10 Dec 2021 12:35:55: #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 12:35:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:35:57: 8000000 INFO @ Fri, 10 Dec 2021 12:36:03: 9000000 INFO @ Fri, 10 Dec 2021 12:36:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:36:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:36:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.05_summits.bed INFO @ Fri, 10 Dec 2021 12:36:05: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1978 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:36:09: 10000000 INFO @ Fri, 10 Dec 2021 12:36:15: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:36:21: 12000000 INFO @ Fri, 10 Dec 2021 12:36:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:36:27: 13000000 INFO @ Fri, 10 Dec 2021 12:36:33: 14000000 INFO @ Fri, 10 Dec 2021 12:36:36: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:36:36: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:36:36: #1 total tags in treatment: 14375928 INFO @ Fri, 10 Dec 2021 12:36:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:36:36: #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 12:36:36: #1 tags after filtering in treatment: 14375928 INFO @ Fri, 10 Dec 2021 12:36:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:36:36: #1 finished! INFO @ Fri, 10 Dec 2021 12:36:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:36:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:36:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:36:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.10_summits.bed INFO @ Fri, 10 Dec 2021 12:36:37: Done! INFO @ Fri, 10 Dec 2021 12:36:37: #2 number of paired peaks: 249 WARNING @ Fri, 10 Dec 2021 12:36:37: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Fri, 10 Dec 2021 12:36:37: start model_add_line... pass1 - making usageList (10 chroms): 1 millis INFO @ Fri, 10 Dec 2021 12:36:37: start X-correlation... pass2 - checking and writing primary data (1459 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:36:37: end of X-cor INFO @ Fri, 10 Dec 2021 12:36:37: #2 finished! INFO @ Fri, 10 Dec 2021 12:36:37: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:36:37: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 10 Dec 2021 12:36:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.20_model.r WARNING @ Fri, 10 Dec 2021 12:36:37: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:36:37: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 10 Dec 2021 12:36:37: #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 12:36:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:36:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:37:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688947/SRX8688947.20_summits.bed INFO @ Fri, 10 Dec 2021 12:37:20: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1137 records, 4 fields): 3 millis CompletedMACS2peakCalling