Job ID = 12265375 SRX = SRX6817533 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18440072 spots for SRR10084524/SRR10084524.sra Written 18440072 spots for SRR10084524/SRR10084524.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265643 ("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: 00:43:02 18440072 reads; of these: 18440072 (100.00%) were paired; of these: 8327146 (45.16%) aligned concordantly 0 times 7918180 (42.94%) aligned concordantly exactly 1 time 2194746 (11.90%) aligned concordantly >1 times ---- 8327146 pairs aligned concordantly 0 times; of these: 2244255 (26.95%) aligned discordantly 1 time ---- 6082891 pairs aligned 0 times concordantly or discordantly; of these: 12165782 mates make up the pairs; of these: 10177047 (83.65%) aligned 0 times 596950 (4.91%) aligned exactly 1 time 1391785 (11.44%) aligned >1 times 72.41% overall alignment rate Time searching: 00:43:02 Overall time: 00:43:02 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 20 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] 2153513 / 12287932 = 0.1753 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.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, 03 Apr 2021 07:43:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:43:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:43:57: 1000000 INFO @ Sat, 03 Apr 2021 07:44:05: 2000000 INFO @ Sat, 03 Apr 2021 07:44:12: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:44:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.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, 03 Apr 2021 07:44:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:44:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:44:20: 4000000 INFO @ Sat, 03 Apr 2021 07:44:28: 1000000 INFO @ Sat, 03 Apr 2021 07:44:28: 5000000 INFO @ Sat, 03 Apr 2021 07:44:37: 6000000 INFO @ Sat, 03 Apr 2021 07:44:37: 2000000 INFO @ Sat, 03 Apr 2021 07:44:45: 7000000 INFO @ Sat, 03 Apr 2021 07:44:46: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:44:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.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, 03 Apr 2021 07:44:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:44:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:44:53: 8000000 INFO @ Sat, 03 Apr 2021 07:44:56: 4000000 INFO @ Sat, 03 Apr 2021 07:44:58: 1000000 INFO @ Sat, 03 Apr 2021 07:45:01: 9000000 INFO @ Sat, 03 Apr 2021 07:45:05: 5000000 INFO @ Sat, 03 Apr 2021 07:45:08: 2000000 INFO @ Sat, 03 Apr 2021 07:45:10: 10000000 INFO @ Sat, 03 Apr 2021 07:45:14: 6000000 INFO @ Sat, 03 Apr 2021 07:45:18: 11000000 INFO @ Sat, 03 Apr 2021 07:45:18: 3000000 INFO @ Sat, 03 Apr 2021 07:45:23: 7000000 INFO @ Sat, 03 Apr 2021 07:45:26: 12000000 INFO @ Sat, 03 Apr 2021 07:45:28: 4000000 INFO @ Sat, 03 Apr 2021 07:45:32: 8000000 INFO @ Sat, 03 Apr 2021 07:45:35: 13000000 INFO @ Sat, 03 Apr 2021 07:45:37: 5000000 INFO @ Sat, 03 Apr 2021 07:45:41: 9000000 INFO @ Sat, 03 Apr 2021 07:45:43: 14000000 INFO @ Sat, 03 Apr 2021 07:45:47: 6000000 INFO @ Sat, 03 Apr 2021 07:45:50: 10000000 INFO @ Sat, 03 Apr 2021 07:45:51: 15000000 INFO @ Sat, 03 Apr 2021 07:45:57: 7000000 INFO @ Sat, 03 Apr 2021 07:45:59: 16000000 INFO @ Sat, 03 Apr 2021 07:46:00: 11000000 INFO @ Sat, 03 Apr 2021 07:46:06: 8000000 INFO @ Sat, 03 Apr 2021 07:46:07: 17000000 INFO @ Sat, 03 Apr 2021 07:46:10: 12000000 INFO @ Sat, 03 Apr 2021 07:46:15: 18000000 INFO @ Sat, 03 Apr 2021 07:46:16: 9000000 INFO @ Sat, 03 Apr 2021 07:46:19: 13000000 INFO @ Sat, 03 Apr 2021 07:46:23: 19000000 INFO @ Sat, 03 Apr 2021 07:46:26: 10000000 INFO @ Sat, 03 Apr 2021 07:46:28: 14000000 INFO @ Sat, 03 Apr 2021 07:46:32: 20000000 INFO @ Sat, 03 Apr 2021 07:46:35: 11000000 INFO @ Sat, 03 Apr 2021 07:46:37: 15000000 INFO @ Sat, 03 Apr 2021 07:46:40: 21000000 INFO @ Sat, 03 Apr 2021 07:46:45: 12000000 INFO @ Sat, 03 Apr 2021 07:46:46: 16000000 INFO @ Sat, 03 Apr 2021 07:46:48: 22000000 INFO @ Sat, 03 Apr 2021 07:46:52: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 07:46:52: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 07:46:52: #1 total tags in treatment: 8209555 INFO @ Sat, 03 Apr 2021 07:46:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:46:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:46:52: #1 tags after filtering in treatment: 7040161 INFO @ Sat, 03 Apr 2021 07:46:52: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 07:46:52: #1 finished! INFO @ Sat, 03 Apr 2021 07:46:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:46:52: #2 number of paired peaks: 258 WARNING @ Sat, 03 Apr 2021 07:46:52: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sat, 03 Apr 2021 07:46:52: start model_add_line... INFO @ Sat, 03 Apr 2021 07:46:52: start X-correlation... INFO @ Sat, 03 Apr 2021 07:46:52: end of X-cor INFO @ Sat, 03 Apr 2021 07:46:52: #2 finished! INFO @ Sat, 03 Apr 2021 07:46:52: #2 predicted fragment length is 231 bps INFO @ Sat, 03 Apr 2021 07:46:52: #2 alternative fragment length(s) may be 231 bps INFO @ Sat, 03 Apr 2021 07:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.05_model.r WARNING @ Sat, 03 Apr 2021 07:46:52: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:46:52: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Sat, 03 Apr 2021 07:46:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:46:52: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:46:54: 13000000 INFO @ Sat, 03 Apr 2021 07:46:55: 17000000 INFO @ Sat, 03 Apr 2021 07:47:04: 14000000 INFO @ Sat, 03 Apr 2021 07:47:04: 18000000 INFO @ Sat, 03 Apr 2021 07:47:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:47:13: 15000000 INFO @ Sat, 03 Apr 2021 07:47:13: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:47:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:47:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:47:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.05_summits.bed INFO @ Sat, 03 Apr 2021 07:47:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3847 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:47:22: 16000000 INFO @ Sat, 03 Apr 2021 07:47:23: 20000000 INFO @ Sat, 03 Apr 2021 07:47:31: 17000000 INFO @ Sat, 03 Apr 2021 07:47:32: 21000000 INFO @ Sat, 03 Apr 2021 07:47:40: 18000000 INFO @ Sat, 03 Apr 2021 07:47:41: 22000000 INFO @ Sat, 03 Apr 2021 07:47:45: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 07:47:45: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 07:47:45: #1 total tags in treatment: 8209555 INFO @ Sat, 03 Apr 2021 07:47:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:47:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:47:45: #1 tags after filtering in treatment: 7040161 INFO @ Sat, 03 Apr 2021 07:47:45: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 07:47:45: #1 finished! INFO @ Sat, 03 Apr 2021 07:47:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:47:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:47:46: #2 number of paired peaks: 258 WARNING @ Sat, 03 Apr 2021 07:47:46: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sat, 03 Apr 2021 07:47:46: start model_add_line... INFO @ Sat, 03 Apr 2021 07:47:46: start X-correlation... INFO @ Sat, 03 Apr 2021 07:47:46: end of X-cor INFO @ Sat, 03 Apr 2021 07:47:46: #2 finished! INFO @ Sat, 03 Apr 2021 07:47:46: #2 predicted fragment length is 231 bps INFO @ Sat, 03 Apr 2021 07:47:46: #2 alternative fragment length(s) may be 231 bps INFO @ Sat, 03 Apr 2021 07:47:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.10_model.r WARNING @ Sat, 03 Apr 2021 07:47:46: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:47:46: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Sat, 03 Apr 2021 07:47:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:47:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:47:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:47:50: 19000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:47:59: 20000000 INFO @ Sat, 03 Apr 2021 07:48:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:48:08: 21000000 INFO @ Sat, 03 Apr 2021 07:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:48:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:48:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.10_summits.bed INFO @ Sat, 03 Apr 2021 07:48:14: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (921 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:48:17: 22000000 INFO @ Sat, 03 Apr 2021 07:48:20: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 07:48:20: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 07:48:20: #1 total tags in treatment: 8209555 INFO @ Sat, 03 Apr 2021 07:48:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:48:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:48:20: #1 tags after filtering in treatment: 7040161 INFO @ Sat, 03 Apr 2021 07:48:20: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 07:48:20: #1 finished! INFO @ Sat, 03 Apr 2021 07:48:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:48:21: #2 number of paired peaks: 258 WARNING @ Sat, 03 Apr 2021 07:48:21: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sat, 03 Apr 2021 07:48:21: start model_add_line... INFO @ Sat, 03 Apr 2021 07:48:21: start X-correlation... INFO @ Sat, 03 Apr 2021 07:48:21: end of X-cor INFO @ Sat, 03 Apr 2021 07:48:21: #2 finished! INFO @ Sat, 03 Apr 2021 07:48:21: #2 predicted fragment length is 231 bps INFO @ Sat, 03 Apr 2021 07:48:21: #2 alternative fragment length(s) may be 231 bps INFO @ Sat, 03 Apr 2021 07:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.20_model.r WARNING @ Sat, 03 Apr 2021 07:48:21: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:48:21: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Sat, 03 Apr 2021 07:48:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:48:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:48:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:48:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:48:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:48:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817533/SRX6817533.20_summits.bed INFO @ Sat, 03 Apr 2021 07:48:47: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 1 millis CompletedMACS2peakCalling