Job ID = 14167057 SRX = SRX10412044 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11075965 spots for SRR14035719/SRR14035719.sra Written 11075965 spots for SRR14035719/SRR14035719.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167573 ("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: 00:50:55 11075965 reads; of these: 11075965 (100.00%) were paired; of these: 1260218 (11.38%) aligned concordantly 0 times 6730450 (60.77%) aligned concordantly exactly 1 time 3085297 (27.86%) aligned concordantly >1 times ---- 1260218 pairs aligned concordantly 0 times; of these: 241453 (19.16%) aligned discordantly 1 time ---- 1018765 pairs aligned 0 times concordantly or discordantly; of these: 2037530 mates make up the pairs; of these: 1482792 (72.77%) aligned 0 times 193903 (9.52%) aligned exactly 1 time 360835 (17.71%) aligned >1 times 93.31% overall alignment rate Time searching: 00:50:55 Overall time: 00:50:55 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 16 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] 2218182 / 10014174 = 0.2215 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 10:28:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.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 10:28:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:28:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:28:54: 1000000 INFO @ Fri, 10 Dec 2021 10:29:03: 2000000 INFO @ Fri, 10 Dec 2021 10:29:12: 3000000 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 10:29:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.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 10:29:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:29:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:29:23: 4000000 INFO @ Fri, 10 Dec 2021 10:29:27: 1000000 INFO @ Fri, 10 Dec 2021 10:29:34: 5000000 INFO @ Fri, 10 Dec 2021 10:29:38: 2000000 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 10:29:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.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 10:29:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:29:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:29:45: 6000000 INFO @ Fri, 10 Dec 2021 10:29:49: 3000000 INFO @ Fri, 10 Dec 2021 10:29:56: 1000000 INFO @ Fri, 10 Dec 2021 10:29:57: 7000000 INFO @ Fri, 10 Dec 2021 10:30:00: 4000000 INFO @ Fri, 10 Dec 2021 10:30:07: 8000000 INFO @ Fri, 10 Dec 2021 10:30:07: 2000000 INFO @ Fri, 10 Dec 2021 10:30:11: 5000000 INFO @ Fri, 10 Dec 2021 10:30:18: 9000000 INFO @ Fri, 10 Dec 2021 10:30:19: 3000000 INFO @ Fri, 10 Dec 2021 10:30:23: 6000000 INFO @ Fri, 10 Dec 2021 10:30:30: 10000000 INFO @ Fri, 10 Dec 2021 10:30:30: 4000000 INFO @ Fri, 10 Dec 2021 10:30:34: 7000000 INFO @ Fri, 10 Dec 2021 10:30:41: 11000000 INFO @ Fri, 10 Dec 2021 10:30:41: 5000000 INFO @ Fri, 10 Dec 2021 10:30:45: 8000000 INFO @ Fri, 10 Dec 2021 10:30:52: 12000000 INFO @ Fri, 10 Dec 2021 10:30:53: 6000000 INFO @ Fri, 10 Dec 2021 10:30:56: 9000000 INFO @ Fri, 10 Dec 2021 10:31:03: 13000000 INFO @ Fri, 10 Dec 2021 10:31:04: 7000000 INFO @ Fri, 10 Dec 2021 10:31:07: 10000000 INFO @ Fri, 10 Dec 2021 10:31:14: 14000000 INFO @ Fri, 10 Dec 2021 10:31:15: 8000000 INFO @ Fri, 10 Dec 2021 10:31:18: 11000000 INFO @ Fri, 10 Dec 2021 10:31:25: 9000000 INFO @ Fri, 10 Dec 2021 10:31:26: 15000000 INFO @ Fri, 10 Dec 2021 10:31:29: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:31:36: 10000000 INFO @ Fri, 10 Dec 2021 10:31:37: 16000000 INFO @ Fri, 10 Dec 2021 10:31:39: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:31:39: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:31:39: #1 total tags in treatment: 7637014 INFO @ Fri, 10 Dec 2021 10:31:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:31:39: #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 10:31:40: #1 tags after filtering in treatment: 7237367 INFO @ Fri, 10 Dec 2021 10:31:40: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 10:31:40: #1 finished! INFO @ Fri, 10 Dec 2021 10:31:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:31:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:31:40: #2 number of paired peaks: 400 WARNING @ Fri, 10 Dec 2021 10:31:40: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 10 Dec 2021 10:31:40: start model_add_line... INFO @ Fri, 10 Dec 2021 10:31:40: start X-correlation... INFO @ Fri, 10 Dec 2021 10:31:40: end of X-cor INFO @ Fri, 10 Dec 2021 10:31:40: #2 finished! INFO @ Fri, 10 Dec 2021 10:31:40: #2 predicted fragment length is 182 bps INFO @ Fri, 10 Dec 2021 10:31:40: #2 alternative fragment length(s) may be 182 bps INFO @ Fri, 10 Dec 2021 10:31:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.05_model.r WARNING @ Fri, 10 Dec 2021 10:31:40: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:31:40: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Fri, 10 Dec 2021 10:31:40: #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 10:31:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:31:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:31:41: 13000000 INFO @ Fri, 10 Dec 2021 10:31:47: 11000000 INFO @ Fri, 10 Dec 2021 10:31:52: 14000000 INFO @ Fri, 10 Dec 2021 10:31:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:31:58: 12000000 INFO @ Fri, 10 Dec 2021 10:32:03: 15000000 INFO @ Fri, 10 Dec 2021 10:32:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:32:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:32:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.05_summits.bed INFO @ Fri, 10 Dec 2021 10:32:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3067 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:32:09: 13000000 INFO @ Fri, 10 Dec 2021 10:32:14: 16000000 INFO @ Fri, 10 Dec 2021 10:32:17: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:32:17: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:32:17: #1 total tags in treatment: 7637014 INFO @ Fri, 10 Dec 2021 10:32:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:32:17: #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 10:32:17: #1 tags after filtering in treatment: 7237367 INFO @ Fri, 10 Dec 2021 10:32:17: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 10:32:17: #1 finished! INFO @ Fri, 10 Dec 2021 10:32:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:32:18: #2 number of paired peaks: 400 WARNING @ Fri, 10 Dec 2021 10:32:18: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 10 Dec 2021 10:32:18: start model_add_line... INFO @ Fri, 10 Dec 2021 10:32:18: start X-correlation... INFO @ Fri, 10 Dec 2021 10:32:18: end of X-cor INFO @ Fri, 10 Dec 2021 10:32:18: #2 finished! INFO @ Fri, 10 Dec 2021 10:32:18: #2 predicted fragment length is 182 bps INFO @ Fri, 10 Dec 2021 10:32:18: #2 alternative fragment length(s) may be 182 bps INFO @ Fri, 10 Dec 2021 10:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.10_model.r WARNING @ Fri, 10 Dec 2021 10:32:18: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:32:18: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Fri, 10 Dec 2021 10:32:18: #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 10:32:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:32:20: 14000000 INFO @ Fri, 10 Dec 2021 10:32:30: 15000000 INFO @ Fri, 10 Dec 2021 10:32:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:32:39: 16000000 INFO @ Fri, 10 Dec 2021 10:32:41: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 10:32:41: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 10:32:41: #1 total tags in treatment: 7637014 INFO @ Fri, 10 Dec 2021 10:32:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:32:41: #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 10:32:41: #1 tags after filtering in treatment: 7237367 INFO @ Fri, 10 Dec 2021 10:32:41: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 10:32:41: #1 finished! INFO @ Fri, 10 Dec 2021 10:32:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:32:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:32:42: #2 number of paired peaks: 400 WARNING @ Fri, 10 Dec 2021 10:32:42: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 10 Dec 2021 10:32:42: start model_add_line... INFO @ Fri, 10 Dec 2021 10:32:42: start X-correlation... INFO @ Fri, 10 Dec 2021 10:32:42: end of X-cor INFO @ Fri, 10 Dec 2021 10:32:42: #2 finished! INFO @ Fri, 10 Dec 2021 10:32:42: #2 predicted fragment length is 182 bps INFO @ Fri, 10 Dec 2021 10:32:42: #2 alternative fragment length(s) may be 182 bps INFO @ Fri, 10 Dec 2021 10:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.20_model.r WARNING @ Fri, 10 Dec 2021 10:32:42: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:32:42: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Fri, 10 Dec 2021 10:32:42: #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 10:32:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:32:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:32:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.10_summits.bed INFO @ Fri, 10 Dec 2021 10:32:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1333 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:32:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:33:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:33:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412044/SRX10412044.20_summits.bed INFO @ Fri, 10 Dec 2021 10:33:07: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (629 records, 4 fields): 2 millis CompletedMACS2peakCalling