Job ID = 14166958 SRX = SRX7541123 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22364096 spots for SRR10871147/SRR10871147.sra Written 22364096 spots for SRR10871147/SRR10871147.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167330 ("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: 00:30:49 22364096 reads; of these: 22364096 (100.00%) were paired; of these: 16146956 (72.20%) aligned concordantly 0 times 4533579 (20.27%) aligned concordantly exactly 1 time 1683561 (7.53%) aligned concordantly >1 times ---- 16146956 pairs aligned concordantly 0 times; of these: 720249 (4.46%) aligned discordantly 1 time ---- 15426707 pairs aligned 0 times concordantly or discordantly; of these: 30853414 mates make up the pairs; of these: 28584872 (92.65%) aligned 0 times 1312327 (4.25%) aligned exactly 1 time 956215 (3.10%) aligned >1 times 36.09% overall alignment rate Time searching: 00:30:49 Overall time: 00:30:49 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 909360 / 6809334 = 0.1335 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 08:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.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 08:44:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:44:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:44:20: 1000000 INFO @ Fri, 10 Dec 2021 08:44:30: 2000000 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 08:44:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.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 08:44:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:44:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:44:40: 3000000 INFO @ Fri, 10 Dec 2021 08:44:50: 1000000 INFO @ Fri, 10 Dec 2021 08:44:51: 4000000 INFO @ Fri, 10 Dec 2021 08:45:01: 2000000 INFO @ Fri, 10 Dec 2021 08:45:02: 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 08:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.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 08:45:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:45:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:45:11: 3000000 INFO @ Fri, 10 Dec 2021 08:45:13: 6000000 INFO @ Fri, 10 Dec 2021 08:45:21: 1000000 INFO @ Fri, 10 Dec 2021 08:45:21: 4000000 INFO @ Fri, 10 Dec 2021 08:45:25: 7000000 INFO @ Fri, 10 Dec 2021 08:45:32: 5000000 INFO @ Fri, 10 Dec 2021 08:45:32: 2000000 INFO @ Fri, 10 Dec 2021 08:45:36: 8000000 INFO @ Fri, 10 Dec 2021 08:45:42: 6000000 INFO @ Fri, 10 Dec 2021 08:45:44: 3000000 INFO @ Fri, 10 Dec 2021 08:45:48: 9000000 INFO @ Fri, 10 Dec 2021 08:45:53: 7000000 INFO @ Fri, 10 Dec 2021 08:45:55: 4000000 INFO @ Fri, 10 Dec 2021 08:45:59: 10000000 INFO @ Fri, 10 Dec 2021 08:46:03: 8000000 INFO @ Fri, 10 Dec 2021 08:46:07: 5000000 INFO @ Fri, 10 Dec 2021 08:46:11: 11000000 INFO @ Fri, 10 Dec 2021 08:46:13: 9000000 INFO @ Fri, 10 Dec 2021 08:46:18: 6000000 INFO @ Fri, 10 Dec 2021 08:46:22: 12000000 INFO @ Fri, 10 Dec 2021 08:46:24: 10000000 INFO @ Fri, 10 Dec 2021 08:46:30: 7000000 INFO @ Fri, 10 Dec 2021 08:46:34: 13000000 INFO @ Fri, 10 Dec 2021 08:46:34: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:46:41: 8000000 INFO @ Fri, 10 Dec 2021 08:46:45: 14000000 INFO @ Fri, 10 Dec 2021 08:46:45: 12000000 INFO @ Fri, 10 Dec 2021 08:46:49: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:46:49: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:46:49: #1 total tags in treatment: 5334687 INFO @ Fri, 10 Dec 2021 08:46:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:46:49: #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 08:46:49: #1 tags after filtering in treatment: 4979260 INFO @ Fri, 10 Dec 2021 08:46:49: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 08:46:49: #1 finished! INFO @ Fri, 10 Dec 2021 08:46:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:46:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:46:49: #2 number of paired peaks: 335 WARNING @ Fri, 10 Dec 2021 08:46:49: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 10 Dec 2021 08:46:49: start model_add_line... INFO @ Fri, 10 Dec 2021 08:46:50: start X-correlation... INFO @ Fri, 10 Dec 2021 08:46:50: end of X-cor INFO @ Fri, 10 Dec 2021 08:46:50: #2 finished! INFO @ Fri, 10 Dec 2021 08:46:50: #2 predicted fragment length is 137 bps INFO @ Fri, 10 Dec 2021 08:46:50: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 10 Dec 2021 08:46:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.05_model.r WARNING @ Fri, 10 Dec 2021 08:46:50: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:46:50: #2 You may need to consider one of the other alternative d(s): 137 WARNING @ Fri, 10 Dec 2021 08:46:50: #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 08:46:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:46:53: 9000000 INFO @ Fri, 10 Dec 2021 08:46:56: 13000000 INFO @ Fri, 10 Dec 2021 08:47:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:47:04: 10000000 INFO @ Fri, 10 Dec 2021 08:47:06: 14000000 INFO @ Fri, 10 Dec 2021 08:47:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:47:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:47:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.05_summits.bed INFO @ Fri, 10 Dec 2021 08:47:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (903 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:47:09: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:47:09: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:47:09: #1 total tags in treatment: 5334687 INFO @ Fri, 10 Dec 2021 08:47:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:47:09: #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 08:47:09: #1 tags after filtering in treatment: 4979260 INFO @ Fri, 10 Dec 2021 08:47:09: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 08:47:09: #1 finished! INFO @ Fri, 10 Dec 2021 08:47:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:47:10: #2 number of paired peaks: 335 WARNING @ Fri, 10 Dec 2021 08:47:10: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 10 Dec 2021 08:47:10: start model_add_line... INFO @ Fri, 10 Dec 2021 08:47:10: start X-correlation... INFO @ Fri, 10 Dec 2021 08:47:10: end of X-cor INFO @ Fri, 10 Dec 2021 08:47:10: #2 finished! INFO @ Fri, 10 Dec 2021 08:47:10: #2 predicted fragment length is 137 bps INFO @ Fri, 10 Dec 2021 08:47:10: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 10 Dec 2021 08:47:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.10_model.r WARNING @ Fri, 10 Dec 2021 08:47:10: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:47:10: #2 You may need to consider one of the other alternative d(s): 137 WARNING @ Fri, 10 Dec 2021 08:47:10: #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 08:47:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:47:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:47:15: 11000000 INFO @ Fri, 10 Dec 2021 08:47:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:47:26: 12000000 INFO @ Fri, 10 Dec 2021 08:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.10_summits.bed INFO @ Fri, 10 Dec 2021 08:47:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:47:36: 13000000 INFO @ Fri, 10 Dec 2021 08:47:46: 14000000 INFO @ Fri, 10 Dec 2021 08:47:50: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:47:50: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:47:50: #1 total tags in treatment: 5334687 INFO @ Fri, 10 Dec 2021 08:47:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:47:50: #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 08:47:50: #1 tags after filtering in treatment: 4979260 INFO @ Fri, 10 Dec 2021 08:47:50: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 08:47:50: #1 finished! INFO @ Fri, 10 Dec 2021 08:47:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:47:50: #2 number of paired peaks: 335 WARNING @ Fri, 10 Dec 2021 08:47:50: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 10 Dec 2021 08:47:50: start model_add_line... INFO @ Fri, 10 Dec 2021 08:47:50: start X-correlation... INFO @ Fri, 10 Dec 2021 08:47:50: end of X-cor INFO @ Fri, 10 Dec 2021 08:47:50: #2 finished! INFO @ Fri, 10 Dec 2021 08:47:50: #2 predicted fragment length is 137 bps INFO @ Fri, 10 Dec 2021 08:47:50: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 10 Dec 2021 08:47:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.20_model.r WARNING @ Fri, 10 Dec 2021 08:47:50: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:47:50: #2 You may need to consider one of the other alternative d(s): 137 WARNING @ Fri, 10 Dec 2021 08:47:50: #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 08:47:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:47:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:48:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:48:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:48:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:48:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541123/SRX7541123.20_summits.bed INFO @ Fri, 10 Dec 2021 08:48:07: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling