Job ID = 14171486 SRX = SRX10971119 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:48:17 prefetch.2.10.7: 1) Downloading 'SRR14631243'... 2021-12-11T02:48:17 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:48:41 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:48:41 prefetch.2.10.7: 1) 'SRR14631243' was downloaded successfully 2021-12-11T02:48:41 prefetch.2.10.7: 'SRR14631243' has 0 unresolved dependencies Read 28992234 spots for SRR14631243/SRR14631243.sra Written 28992234 spots for SRR14631243/SRR14631243.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172447 ("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: 01:49:12 28992234 reads; of these: 28992234 (100.00%) were paired; of these: 3896668 (13.44%) aligned concordantly 0 times 18735269 (64.62%) aligned concordantly exactly 1 time 6360297 (21.94%) aligned concordantly >1 times ---- 3896668 pairs aligned concordantly 0 times; of these: 141627 (3.63%) aligned discordantly 1 time ---- 3755041 pairs aligned 0 times concordantly or discordantly; of these: 7510082 mates make up the pairs; of these: 5101432 (67.93%) aligned 0 times 843348 (11.23%) aligned exactly 1 time 1565302 (20.84%) aligned >1 times 91.20% overall alignment rate Time searching: 01:49:13 Overall time: 01:49:13 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 24 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] 16573156 / 24979123 = 0.6635 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 13:52:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.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 13:52:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:52:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:52:20: 1000000 INFO @ Sat, 11 Dec 2021 13:52:25: 2000000 INFO @ Sat, 11 Dec 2021 13:52:30: 3000000 INFO @ Sat, 11 Dec 2021 13:52:36: 4000000 INFO @ Sat, 11 Dec 2021 13:52:41: 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 @ Sat, 11 Dec 2021 13:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.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 13:52:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:52:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:52:46: 6000000 INFO @ Sat, 11 Dec 2021 13:52:51: 1000000 INFO @ Sat, 11 Dec 2021 13:52:52: 7000000 INFO @ Sat, 11 Dec 2021 13:52:58: 2000000 INFO @ Sat, 11 Dec 2021 13:52:58: 8000000 INFO @ Sat, 11 Dec 2021 13:53:03: 9000000 INFO @ Sat, 11 Dec 2021 13:53:04: 3000000 INFO @ Sat, 11 Dec 2021 13:53:09: 10000000 INFO @ Sat, 11 Dec 2021 13:53:11: 4000000 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 13:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.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 13:53:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:53:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:53:14: 11000000 INFO @ Sat, 11 Dec 2021 13:53:18: 5000000 INFO @ Sat, 11 Dec 2021 13:53:20: 12000000 INFO @ Sat, 11 Dec 2021 13:53:20: 1000000 INFO @ Sat, 11 Dec 2021 13:53:25: 6000000 INFO @ Sat, 11 Dec 2021 13:53:26: 13000000 INFO @ Sat, 11 Dec 2021 13:53:26: 2000000 INFO @ Sat, 11 Dec 2021 13:53:32: 14000000 INFO @ Sat, 11 Dec 2021 13:53:32: 7000000 INFO @ Sat, 11 Dec 2021 13:53:32: 3000000 INFO @ Sat, 11 Dec 2021 13:53:37: 15000000 INFO @ Sat, 11 Dec 2021 13:53:39: 8000000 INFO @ Sat, 11 Dec 2021 13:53:39: 4000000 INFO @ Sat, 11 Dec 2021 13:53:43: 16000000 INFO @ Sat, 11 Dec 2021 13:53:45: 5000000 INFO @ Sat, 11 Dec 2021 13:53:45: 9000000 INFO @ Sat, 11 Dec 2021 13:53:49: 17000000 INFO @ Sat, 11 Dec 2021 13:53:50: 6000000 INFO @ Sat, 11 Dec 2021 13:53:52: 10000000 INFO @ Sat, 11 Dec 2021 13:53:55: 18000000 INFO @ Sat, 11 Dec 2021 13:53:56: 7000000 INFO @ Sat, 11 Dec 2021 13:53:59: 11000000 INFO @ Sat, 11 Dec 2021 13:54:00: 19000000 INFO @ Sat, 11 Dec 2021 13:54:02: 8000000 INFO @ Sat, 11 Dec 2021 13:54:05: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:54:05: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:54:05: #1 total tags in treatment: 8565121 INFO @ Sat, 11 Dec 2021 13:54:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:54:05: #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 13:54:05: #1 tags after filtering in treatment: 7489938 INFO @ Sat, 11 Dec 2021 13:54:05: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 13:54:05: #1 finished! INFO @ Sat, 11 Dec 2021 13:54:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:54:05: #2 number of paired peaks: 734 WARNING @ Sat, 11 Dec 2021 13:54:05: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Sat, 11 Dec 2021 13:54:05: start model_add_line... INFO @ Sat, 11 Dec 2021 13:54:05: start X-correlation... INFO @ Sat, 11 Dec 2021 13:54:05: end of X-cor INFO @ Sat, 11 Dec 2021 13:54:05: #2 finished! INFO @ Sat, 11 Dec 2021 13:54:05: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 13:54:05: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 11 Dec 2021 13:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.05_model.r WARNING @ Sat, 11 Dec 2021 13:54:05: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:54:05: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 11 Dec 2021 13:54:05: #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 13:54:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:54:06: 12000000 INFO @ Sat, 11 Dec 2021 13:54:08: 9000000 INFO @ Sat, 11 Dec 2021 13:54:13: 13000000 INFO @ Sat, 11 Dec 2021 13:54:13: 10000000 INFO @ Sat, 11 Dec 2021 13:54:19: 11000000 INFO @ Sat, 11 Dec 2021 13:54:20: 14000000 INFO @ Sat, 11 Dec 2021 13:54:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:54:25: 12000000 INFO @ Sat, 11 Dec 2021 13:54:27: 15000000 INFO @ Sat, 11 Dec 2021 13:54:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:54:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:54:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.05_summits.bed INFO @ Sat, 11 Dec 2021 13:54:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5606 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:54:32: 13000000 INFO @ Sat, 11 Dec 2021 13:54:33: 16000000 INFO @ Sat, 11 Dec 2021 13:54:38: 14000000 INFO @ Sat, 11 Dec 2021 13:54:40: 17000000 INFO @ Sat, 11 Dec 2021 13:54:44: 15000000 INFO @ Sat, 11 Dec 2021 13:54:47: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:54:50: 16000000 INFO @ Sat, 11 Dec 2021 13:54:54: 19000000 INFO @ Sat, 11 Dec 2021 13:54:55: 17000000 INFO @ Sat, 11 Dec 2021 13:54:59: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:54:59: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:54:59: #1 total tags in treatment: 8565121 INFO @ Sat, 11 Dec 2021 13:54:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:54:59: #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 13:54:59: #1 tags after filtering in treatment: 7489938 INFO @ Sat, 11 Dec 2021 13:54:59: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 13:54:59: #1 finished! INFO @ Sat, 11 Dec 2021 13:54:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:55:00: #2 number of paired peaks: 734 WARNING @ Sat, 11 Dec 2021 13:55:00: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Sat, 11 Dec 2021 13:55:00: start model_add_line... INFO @ Sat, 11 Dec 2021 13:55:00: start X-correlation... INFO @ Sat, 11 Dec 2021 13:55:00: end of X-cor INFO @ Sat, 11 Dec 2021 13:55:00: #2 finished! INFO @ Sat, 11 Dec 2021 13:55:00: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 13:55:00: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 11 Dec 2021 13:55:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.10_model.r WARNING @ Sat, 11 Dec 2021 13:55:00: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:55:00: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 11 Dec 2021 13:55:00: #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 13:55:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:55:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:55:01: 18000000 INFO @ Sat, 11 Dec 2021 13:55:06: 19000000 INFO @ Sat, 11 Dec 2021 13:55:10: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 13:55:10: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 13:55:10: #1 total tags in treatment: 8565121 INFO @ Sat, 11 Dec 2021 13:55:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:55:10: #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 13:55:10: #1 tags after filtering in treatment: 7489938 INFO @ Sat, 11 Dec 2021 13:55:10: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 13:55:10: #1 finished! INFO @ Sat, 11 Dec 2021 13:55:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:55:11: #2 number of paired peaks: 734 WARNING @ Sat, 11 Dec 2021 13:55:11: Fewer paired peaks (734) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 734 pairs to build model! INFO @ Sat, 11 Dec 2021 13:55:11: start model_add_line... INFO @ Sat, 11 Dec 2021 13:55:11: start X-correlation... INFO @ Sat, 11 Dec 2021 13:55:11: end of X-cor INFO @ Sat, 11 Dec 2021 13:55:11: #2 finished! INFO @ Sat, 11 Dec 2021 13:55:11: #2 predicted fragment length is 149 bps INFO @ Sat, 11 Dec 2021 13:55:11: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 11 Dec 2021 13:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.20_model.r WARNING @ Sat, 11 Dec 2021 13:55:11: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:55:11: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 11 Dec 2021 13:55:11: #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 13:55:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:55:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:55:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:55:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.10_summits.bed INFO @ Sat, 11 Dec 2021 13:55:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2906 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:55:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:55:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:55:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:55:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971119/SRX10971119.20_summits.bed INFO @ Sat, 11 Dec 2021 13:55:34: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1221 records, 4 fields): 3 millis CompletedMACS2peakCalling