Job ID = 14168998 SRX = SRX9910788 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31872387 spots for SRR13498859/SRR13498859.sra Written 31872387 spots for SRR13498859/SRR13498859.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170300 ("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: 01:23:21 31872387 reads; of these: 31872387 (100.00%) were paired; of these: 11221008 (35.21%) aligned concordantly 0 times 12130758 (38.06%) aligned concordantly exactly 1 time 8520621 (26.73%) aligned concordantly >1 times ---- 11221008 pairs aligned concordantly 0 times; of these: 1459176 (13.00%) aligned discordantly 1 time ---- 9761832 pairs aligned 0 times concordantly or discordantly; of these: 19523664 mates make up the pairs; of these: 15148042 (77.59%) aligned 0 times 446959 (2.29%) aligned exactly 1 time 3928663 (20.12%) aligned >1 times 76.24% overall alignment rate Time searching: 01:23:21 Overall time: 01:23:21 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 36 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] 10537910 / 21983642 = 0.4794 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 @ Sat, 11 Dec 2021 00:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.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 @ Sat, 11 Dec 2021 00:20:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:20:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:20:41: 1000000 INFO @ Sat, 11 Dec 2021 00:20:48: 2000000 INFO @ Sat, 11 Dec 2021 00:20:56: 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 @ Sat, 11 Dec 2021 00:21:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.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 @ Sat, 11 Dec 2021 00:21:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:21:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:21:04: 4000000 INFO @ Sat, 11 Dec 2021 00:21:13: 5000000 INFO @ Sat, 11 Dec 2021 00:21:18: 1000000 INFO @ Sat, 11 Dec 2021 00:21:22: 6000000 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 @ Sat, 11 Dec 2021 00:21:32: 7000000 INFO @ Sat, 11 Dec 2021 00:21:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.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 @ Sat, 11 Dec 2021 00:21:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:21:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:21:32: 2000000 INFO @ Sat, 11 Dec 2021 00:21:41: 8000000 INFO @ Sat, 11 Dec 2021 00:21:42: 1000000 INFO @ Sat, 11 Dec 2021 00:21:46: 3000000 INFO @ Sat, 11 Dec 2021 00:21:51: 9000000 INFO @ Sat, 11 Dec 2021 00:21:51: 2000000 INFO @ Sat, 11 Dec 2021 00:22:01: 10000000 INFO @ Sat, 11 Dec 2021 00:22:01: 4000000 INFO @ Sat, 11 Dec 2021 00:22:01: 3000000 INFO @ Sat, 11 Dec 2021 00:22:11: 11000000 INFO @ Sat, 11 Dec 2021 00:22:11: 4000000 INFO @ Sat, 11 Dec 2021 00:22:17: 5000000 INFO @ Sat, 11 Dec 2021 00:22:20: 12000000 INFO @ Sat, 11 Dec 2021 00:22:21: 5000000 INFO @ Sat, 11 Dec 2021 00:22:30: 13000000 INFO @ Sat, 11 Dec 2021 00:22:32: 6000000 INFO @ Sat, 11 Dec 2021 00:22:33: 6000000 INFO @ Sat, 11 Dec 2021 00:22:40: 14000000 INFO @ Sat, 11 Dec 2021 00:22:42: 7000000 INFO @ Sat, 11 Dec 2021 00:22:48: 7000000 INFO @ Sat, 11 Dec 2021 00:22:49: 15000000 INFO @ Sat, 11 Dec 2021 00:22:51: 8000000 INFO @ Sat, 11 Dec 2021 00:22:59: 16000000 INFO @ Sat, 11 Dec 2021 00:23:01: 9000000 INFO @ Sat, 11 Dec 2021 00:23:02: 8000000 INFO @ Sat, 11 Dec 2021 00:23:08: 17000000 INFO @ Sat, 11 Dec 2021 00:23:10: 10000000 INFO @ Sat, 11 Dec 2021 00:23:17: 9000000 INFO @ Sat, 11 Dec 2021 00:23:17: 18000000 INFO @ Sat, 11 Dec 2021 00:23:20: 11000000 INFO @ Sat, 11 Dec 2021 00:23:26: 19000000 INFO @ Sat, 11 Dec 2021 00:23:29: 12000000 INFO @ Sat, 11 Dec 2021 00:23:32: 10000000 INFO @ Sat, 11 Dec 2021 00:23:35: 20000000 INFO @ Sat, 11 Dec 2021 00:23:39: 13000000 INFO @ Sat, 11 Dec 2021 00:23:44: 21000000 INFO @ Sat, 11 Dec 2021 00:23:48: 11000000 INFO @ Sat, 11 Dec 2021 00:23:48: 14000000 INFO @ Sat, 11 Dec 2021 00:23:53: 22000000 INFO @ Sat, 11 Dec 2021 00:23:58: 15000000 INFO @ Sat, 11 Dec 2021 00:24:03: 23000000 INFO @ Sat, 11 Dec 2021 00:24:03: 12000000 INFO @ Sat, 11 Dec 2021 00:24:07: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 00:24:12: 24000000 INFO @ Sat, 11 Dec 2021 00:24:16: 17000000 INFO @ Sat, 11 Dec 2021 00:24:18: 13000000 INFO @ Sat, 11 Dec 2021 00:24:22: 25000000 INFO @ Sat, 11 Dec 2021 00:24:25: 18000000 INFO @ Sat, 11 Dec 2021 00:24:31: 26000000 INFO @ Sat, 11 Dec 2021 00:24:32: 14000000 INFO @ Sat, 11 Dec 2021 00:24:34: 19000000 INFO @ Sat, 11 Dec 2021 00:24:40: 27000000 INFO @ Sat, 11 Dec 2021 00:24:44: 20000000 INFO @ Sat, 11 Dec 2021 00:24:45: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:24:45: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:24:45: #1 total tags in treatment: 10593455 INFO @ Sat, 11 Dec 2021 00:24:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:24:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 00:24:45: #1 tags after filtering in treatment: 8502689 INFO @ Sat, 11 Dec 2021 00:24:45: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 00:24:45: #1 finished! INFO @ Sat, 11 Dec 2021 00:24:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:24:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:24:46: #2 number of paired peaks: 216 WARNING @ Sat, 11 Dec 2021 00:24:46: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sat, 11 Dec 2021 00:24:46: start model_add_line... INFO @ Sat, 11 Dec 2021 00:24:46: start X-correlation... INFO @ Sat, 11 Dec 2021 00:24:46: end of X-cor INFO @ Sat, 11 Dec 2021 00:24:46: #2 finished! INFO @ Sat, 11 Dec 2021 00:24:46: #2 predicted fragment length is 215 bps INFO @ Sat, 11 Dec 2021 00:24:46: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 11 Dec 2021 00:24:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.05_model.r WARNING @ Sat, 11 Dec 2021 00:24:46: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:24:46: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 11 Dec 2021 00:24:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 00:24:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:24:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:24:47: 15000000 INFO @ Sat, 11 Dec 2021 00:24:53: 21000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 00:25:02: 22000000 INFO @ Sat, 11 Dec 2021 00:25:03: 16000000 INFO @ Sat, 11 Dec 2021 00:25:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:25:11: 23000000 INFO @ Sat, 11 Dec 2021 00:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.05_peaks.xls INFO @ Sat, 11 Dec 2021 00:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.05_summits.bed INFO @ Sat, 11 Dec 2021 00:25:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2789 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:25:18: 17000000 INFO @ Sat, 11 Dec 2021 00:25:20: 24000000 INFO @ Sat, 11 Dec 2021 00:25:29: 25000000 INFO @ Sat, 11 Dec 2021 00:25:33: 18000000 INFO @ Sat, 11 Dec 2021 00:25:38: 26000000 INFO @ Sat, 11 Dec 2021 00:25:45: 19000000 INFO @ Sat, 11 Dec 2021 00:25:47: 27000000 INFO @ Sat, 11 Dec 2021 00:25:52: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:25:52: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:25:52: #1 total tags in treatment: 10593455 INFO @ Sat, 11 Dec 2021 00:25:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:25:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 00:25:52: #1 tags after filtering in treatment: 8502689 INFO @ Sat, 11 Dec 2021 00:25:52: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 00:25:52: #1 finished! INFO @ Sat, 11 Dec 2021 00:25:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:25:53: #2 number of paired peaks: 216 WARNING @ Sat, 11 Dec 2021 00:25:53: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sat, 11 Dec 2021 00:25:53: start model_add_line... INFO @ Sat, 11 Dec 2021 00:25:53: start X-correlation... INFO @ Sat, 11 Dec 2021 00:25:53: end of X-cor INFO @ Sat, 11 Dec 2021 00:25:53: #2 finished! INFO @ Sat, 11 Dec 2021 00:25:53: #2 predicted fragment length is 215 bps INFO @ Sat, 11 Dec 2021 00:25:53: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 11 Dec 2021 00:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.20_model.r WARNING @ Sat, 11 Dec 2021 00:25:53: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:25:53: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 11 Dec 2021 00:25:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 00:25:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:25:58: 20000000 INFO @ Sat, 11 Dec 2021 00:26:12: 21000000 INFO @ Sat, 11 Dec 2021 00:26:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.20_summits.bed INFO @ Sat, 11 Dec 2021 00:26:24: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (325 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:26:27: 22000000 INFO @ Sat, 11 Dec 2021 00:26:41: 23000000 INFO @ Sat, 11 Dec 2021 00:26:55: 24000000 INFO @ Sat, 11 Dec 2021 00:27:09: 25000000 INFO @ Sat, 11 Dec 2021 00:27:21: 26000000 INFO @ Sat, 11 Dec 2021 00:27:34: 27000000 INFO @ Sat, 11 Dec 2021 00:27:41: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:27:41: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:27:41: #1 total tags in treatment: 10593455 INFO @ Sat, 11 Dec 2021 00:27:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:27:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 00:27:41: #1 tags after filtering in treatment: 8502689 INFO @ Sat, 11 Dec 2021 00:27:41: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 00:27:41: #1 finished! INFO @ Sat, 11 Dec 2021 00:27:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:27:42: #2 number of paired peaks: 216 WARNING @ Sat, 11 Dec 2021 00:27:42: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sat, 11 Dec 2021 00:27:42: start model_add_line... INFO @ Sat, 11 Dec 2021 00:27:42: start X-correlation... INFO @ Sat, 11 Dec 2021 00:27:42: end of X-cor INFO @ Sat, 11 Dec 2021 00:27:42: #2 finished! INFO @ Sat, 11 Dec 2021 00:27:42: #2 predicted fragment length is 215 bps INFO @ Sat, 11 Dec 2021 00:27:42: #2 alternative fragment length(s) may be 215 bps INFO @ Sat, 11 Dec 2021 00:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.10_model.r WARNING @ Sat, 11 Dec 2021 00:27:42: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:27:42: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Sat, 11 Dec 2021 00:27:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 00:27:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:28:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:28:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:28:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:28:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910788/SRX9910788.10_summits.bed INFO @ Sat, 11 Dec 2021 00:28:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (916 records, 4 fields): 3 millis CompletedMACS2peakCalling