Job ID = 14171766 SRX = SRX10386233 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23888530 spots for SRR14009298/SRR14009298.sra Written 23888530 spots for SRR14009298/SRR14009298.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172299 ("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: 00:27:18 23888530 reads; of these: 23888530 (100.00%) were paired; of these: 11539851 (48.31%) aligned concordantly 0 times 8212480 (34.38%) aligned concordantly exactly 1 time 4136199 (17.31%) aligned concordantly >1 times ---- 11539851 pairs aligned concordantly 0 times; of these: 70750 (0.61%) aligned discordantly 1 time ---- 11469101 pairs aligned 0 times concordantly or discordantly; of these: 22938202 mates make up the pairs; of these: 22417529 (97.73%) aligned 0 times 294640 (1.28%) aligned exactly 1 time 226033 (0.99%) aligned >1 times 53.08% overall alignment rate Time searching: 00:27:18 Overall time: 00:27:18 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_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] 3665842 / 12392686 = 0.2958 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 13:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.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 13:19:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:19:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:20:02: 1000000 INFO @ Sat, 11 Dec 2021 13:20:06: 2000000 INFO @ Sat, 11 Dec 2021 13:20:10: 3000000 INFO @ Sat, 11 Dec 2021 13:20:15: 4000000 INFO @ Sat, 11 Dec 2021 13:20:19: 5000000 INFO @ Sat, 11 Dec 2021 13:20:23: 6000000 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 13:20:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.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 13:20:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:20:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:20:28: 7000000 INFO @ Sat, 11 Dec 2021 13:20:32: 8000000 INFO @ Sat, 11 Dec 2021 13:20:32: 1000000 INFO @ Sat, 11 Dec 2021 13:20:37: 9000000 INFO @ Sat, 11 Dec 2021 13:20:37: 2000000 INFO @ Sat, 11 Dec 2021 13:20:42: 10000000 INFO @ Sat, 11 Dec 2021 13:20:42: 3000000 INFO @ Sat, 11 Dec 2021 13:20:46: 11000000 INFO @ Sat, 11 Dec 2021 13:20:47: 4000000 INFO @ Sat, 11 Dec 2021 13:20:51: 12000000 INFO @ Sat, 11 Dec 2021 13:20:52: 5000000 INFO @ Sat, 11 Dec 2021 13:20:55: 13000000 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 13:20:57: 6000000 INFO @ Sat, 11 Dec 2021 13:20:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.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 13:20:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:20:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:21:00: 14000000 INFO @ Sat, 11 Dec 2021 13:21:02: 7000000 INFO @ Sat, 11 Dec 2021 13:21:03: 1000000 INFO @ Sat, 11 Dec 2021 13:21:05: 15000000 INFO @ Sat, 11 Dec 2021 13:21:07: 8000000 INFO @ Sat, 11 Dec 2021 13:21:08: 2000000 INFO @ Sat, 11 Dec 2021 13:21:09: 16000000 INFO @ Sat, 11 Dec 2021 13:21:12: 9000000 INFO @ Sat, 11 Dec 2021 13:21:13: 3000000 INFO @ Sat, 11 Dec 2021 13:21:14: 17000000 INFO @ Sat, 11 Dec 2021 13:21:18: 10000000 INFO @ Sat, 11 Dec 2021 13:21:19: 4000000 INFO @ Sat, 11 Dec 2021 13:21:19: 18000000 INFO @ Sat, 11 Dec 2021 13:21:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:21:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:21:19: #1 total tags in treatment: 8691651 INFO @ Sat, 11 Dec 2021 13:21:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:21:19: #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 13:21:19: #1 tags after filtering in treatment: 7643237 INFO @ Sat, 11 Dec 2021 13:21:19: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 13:21:19: #1 finished! INFO @ Sat, 11 Dec 2021 13:21:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:21:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:21:19: #2 number of paired peaks: 252 WARNING @ Sat, 11 Dec 2021 13:21:19: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 11 Dec 2021 13:21:19: start model_add_line... INFO @ Sat, 11 Dec 2021 13:21:20: start X-correlation... INFO @ Sat, 11 Dec 2021 13:21:20: end of X-cor INFO @ Sat, 11 Dec 2021 13:21:20: #2 finished! INFO @ Sat, 11 Dec 2021 13:21:20: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 13:21:20: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 11 Dec 2021 13:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.05_model.r WARNING @ Sat, 11 Dec 2021 13:21:20: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:21:20: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 11 Dec 2021 13:21:20: #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 13:21:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:21:22: 11000000 INFO @ Sat, 11 Dec 2021 13:21:23: 5000000 INFO @ Sat, 11 Dec 2021 13:21:27: 12000000 INFO @ Sat, 11 Dec 2021 13:21:28: 6000000 INFO @ Sat, 11 Dec 2021 13:21:32: 13000000 INFO @ Sat, 11 Dec 2021 13:21:33: 7000000 INFO @ Sat, 11 Dec 2021 13:21:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:21:37: 14000000 INFO @ Sat, 11 Dec 2021 13:21:38: 8000000 INFO @ Sat, 11 Dec 2021 13:21:43: 15000000 INFO @ Sat, 11 Dec 2021 13:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.05_summits.bed INFO @ Sat, 11 Dec 2021 13:21:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1207 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:21:44: 9000000 INFO @ Sat, 11 Dec 2021 13:21:48: 16000000 INFO @ Sat, 11 Dec 2021 13:21:49: 10000000 INFO @ Sat, 11 Dec 2021 13:21:53: 17000000 INFO @ Sat, 11 Dec 2021 13:21:54: 11000000 INFO @ Sat, 11 Dec 2021 13:21:58: 18000000 INFO @ Sat, 11 Dec 2021 13:21:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:21:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:21:58: #1 total tags in treatment: 8691651 INFO @ Sat, 11 Dec 2021 13:21:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:21:58: #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 13:21:58: #1 tags after filtering in treatment: 7643237 INFO @ Sat, 11 Dec 2021 13:21:58: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 13:21:58: #1 finished! INFO @ Sat, 11 Dec 2021 13:21:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:21:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:21:59: 12000000 INFO @ Sat, 11 Dec 2021 13:21:59: #2 number of paired peaks: 252 WARNING @ Sat, 11 Dec 2021 13:21:59: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 11 Dec 2021 13:21:59: start model_add_line... INFO @ Sat, 11 Dec 2021 13:21:59: start X-correlation... INFO @ Sat, 11 Dec 2021 13:21:59: end of X-cor INFO @ Sat, 11 Dec 2021 13:21:59: #2 finished! INFO @ Sat, 11 Dec 2021 13:21:59: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 13:21:59: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 11 Dec 2021 13:21:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.10_model.r WARNING @ Sat, 11 Dec 2021 13:21:59: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:21:59: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 11 Dec 2021 13:21:59: #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 13:21:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:21:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:22:03: 13000000 INFO @ Sat, 11 Dec 2021 13:22:08: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:22:12: 15000000 INFO @ Sat, 11 Dec 2021 13:22:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:22:17: 16000000 INFO @ Sat, 11 Dec 2021 13:22:22: 17000000 INFO @ Sat, 11 Dec 2021 13:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.10_summits.bed INFO @ Sat, 11 Dec 2021 13:22:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (713 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:22:27: 18000000 INFO @ Sat, 11 Dec 2021 13:22:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:22:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:22:27: #1 total tags in treatment: 8691651 INFO @ Sat, 11 Dec 2021 13:22:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:22:27: #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 13:22:27: #1 tags after filtering in treatment: 7643237 INFO @ Sat, 11 Dec 2021 13:22:27: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 13:22:27: #1 finished! INFO @ Sat, 11 Dec 2021 13:22:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:22:27: #2 number of paired peaks: 252 WARNING @ Sat, 11 Dec 2021 13:22:27: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sat, 11 Dec 2021 13:22:27: start model_add_line... INFO @ Sat, 11 Dec 2021 13:22:27: start X-correlation... INFO @ Sat, 11 Dec 2021 13:22:27: end of X-cor INFO @ Sat, 11 Dec 2021 13:22:27: #2 finished! INFO @ Sat, 11 Dec 2021 13:22:27: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 13:22:27: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 11 Dec 2021 13:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.20_model.r WARNING @ Sat, 11 Dec 2021 13:22:27: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:22:27: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 11 Dec 2021 13:22:27: #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 13:22:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:22:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:22:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:22:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:22:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386233/SRX10386233.20_summits.bed INFO @ Sat, 11 Dec 2021 13:22:51: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (423 records, 4 fields): 2 millis CompletedMACS2peakCalling