Job ID = 12266652 SRX = SRX7806724 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13343950 spots for SRR11186390/SRR11186390.sra Written 13343950 spots for SRR11186390/SRR11186390.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267083 ("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: 00:31:10 13343950 reads; of these: 13343950 (100.00%) were paired; of these: 6177033 (46.29%) aligned concordantly 0 times 5063376 (37.95%) aligned concordantly exactly 1 time 2103541 (15.76%) aligned concordantly >1 times ---- 6177033 pairs aligned concordantly 0 times; of these: 1229194 (19.90%) aligned discordantly 1 time ---- 4947839 pairs aligned 0 times concordantly or discordantly; of these: 9895678 mates make up the pairs; of these: 8347486 (84.35%) aligned 0 times 771978 (7.80%) aligned exactly 1 time 776214 (7.84%) aligned >1 times 68.72% overall alignment rate Time searching: 00:31:10 Overall time: 00:31:10 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 8 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] 1103254 / 8346203 = 0.1322 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 09:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.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 09:44:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:44:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:44:13: 1000000 INFO @ Sat, 03 Apr 2021 09:44:19: 2000000 INFO @ Sat, 03 Apr 2021 09:44:25: 3000000 INFO @ Sat, 03 Apr 2021 09:44:30: 4000000 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 09:44:36: 5000000 INFO @ Sat, 03 Apr 2021 09:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.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 09:44:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:44:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:44:42: 6000000 INFO @ Sat, 03 Apr 2021 09:44:44: 1000000 INFO @ Sat, 03 Apr 2021 09:44:48: 7000000 INFO @ Sat, 03 Apr 2021 09:44:50: 2000000 INFO @ Sat, 03 Apr 2021 09:44:54: 8000000 INFO @ Sat, 03 Apr 2021 09:44:57: 3000000 INFO @ Sat, 03 Apr 2021 09:44:59: 9000000 INFO @ Sat, 03 Apr 2021 09:45:04: 4000000 INFO @ Sat, 03 Apr 2021 09:45:05: 10000000 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 09:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.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 09:45:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:45:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:45:10: 5000000 INFO @ Sat, 03 Apr 2021 09:45:10: 11000000 INFO @ Sat, 03 Apr 2021 09:45:14: 1000000 INFO @ Sat, 03 Apr 2021 09:45:16: 6000000 INFO @ Sat, 03 Apr 2021 09:45:17: 12000000 INFO @ Sat, 03 Apr 2021 09:45:21: 2000000 INFO @ Sat, 03 Apr 2021 09:45:23: 13000000 INFO @ Sat, 03 Apr 2021 09:45:23: 7000000 INFO @ Sat, 03 Apr 2021 09:45:27: 3000000 INFO @ Sat, 03 Apr 2021 09:45:29: 14000000 INFO @ Sat, 03 Apr 2021 09:45:29: 8000000 INFO @ Sat, 03 Apr 2021 09:45:33: 4000000 INFO @ Sat, 03 Apr 2021 09:45:35: 15000000 INFO @ Sat, 03 Apr 2021 09:45:36: 9000000 INFO @ Sat, 03 Apr 2021 09:45:40: 5000000 INFO @ Sat, 03 Apr 2021 09:45:42: 10000000 INFO @ Sat, 03 Apr 2021 09:45:42: 16000000 INFO @ Sat, 03 Apr 2021 09:45:43: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:45:43: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:45:43: #1 total tags in treatment: 6142826 INFO @ Sat, 03 Apr 2021 09:45:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:45:43: #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 09:45:43: #1 tags after filtering in treatment: 5271664 INFO @ Sat, 03 Apr 2021 09:45:43: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 09:45:43: #1 finished! INFO @ Sat, 03 Apr 2021 09:45:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:45:44: #2 number of paired peaks: 732 WARNING @ Sat, 03 Apr 2021 09:45:44: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 03 Apr 2021 09:45:44: start model_add_line... INFO @ Sat, 03 Apr 2021 09:45:44: start X-correlation... INFO @ Sat, 03 Apr 2021 09:45:44: end of X-cor INFO @ Sat, 03 Apr 2021 09:45:44: #2 finished! INFO @ Sat, 03 Apr 2021 09:45:44: #2 predicted fragment length is 150 bps INFO @ Sat, 03 Apr 2021 09:45:44: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 03 Apr 2021 09:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.05_model.r WARNING @ Sat, 03 Apr 2021 09:45:44: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:45:44: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sat, 03 Apr 2021 09:45:44: #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 09:45:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:45:46: 6000000 INFO @ Sat, 03 Apr 2021 09:45:48: 11000000 INFO @ Sat, 03 Apr 2021 09:45:52: 7000000 INFO @ Sat, 03 Apr 2021 09:45:54: 12000000 INFO @ Sat, 03 Apr 2021 09:45:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:45:58: 8000000 INFO @ Sat, 03 Apr 2021 09:45:59: 13000000 INFO @ Sat, 03 Apr 2021 09:46:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:46:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:46:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.05_summits.bed INFO @ Sat, 03 Apr 2021 09:46:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5640 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:46:03: 9000000 INFO @ Sat, 03 Apr 2021 09:46:04: 14000000 INFO @ Sat, 03 Apr 2021 09:46:09: 10000000 INFO @ Sat, 03 Apr 2021 09:46:10: 15000000 INFO @ Sat, 03 Apr 2021 09:46:14: 11000000 INFO @ Sat, 03 Apr 2021 09:46:15: 16000000 INFO @ Sat, 03 Apr 2021 09:46:16: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:46:16: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:46:16: #1 total tags in treatment: 6142826 INFO @ Sat, 03 Apr 2021 09:46:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:46:16: #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 09:46:16: #1 tags after filtering in treatment: 5271664 INFO @ Sat, 03 Apr 2021 09:46:16: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 09:46:16: #1 finished! INFO @ Sat, 03 Apr 2021 09:46:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:46:16: #2 number of paired peaks: 732 WARNING @ Sat, 03 Apr 2021 09:46:16: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 03 Apr 2021 09:46:16: start model_add_line... INFO @ Sat, 03 Apr 2021 09:46:16: start X-correlation... INFO @ Sat, 03 Apr 2021 09:46:16: end of X-cor INFO @ Sat, 03 Apr 2021 09:46:16: #2 finished! INFO @ Sat, 03 Apr 2021 09:46:16: #2 predicted fragment length is 150 bps INFO @ Sat, 03 Apr 2021 09:46:16: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 03 Apr 2021 09:46:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.10_model.r WARNING @ Sat, 03 Apr 2021 09:46:16: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:46:16: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sat, 03 Apr 2021 09:46:16: #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 09:46:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:46:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:46:19: 12000000 INFO @ Sat, 03 Apr 2021 09:46:25: 13000000 INFO @ Sat, 03 Apr 2021 09:46:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:46:30: 14000000 INFO @ Sat, 03 Apr 2021 09:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.10_summits.bed INFO @ Sat, 03 Apr 2021 09:46:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2006 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:46:36: 15000000 INFO @ Sat, 03 Apr 2021 09:46:41: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:46:42: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:46:42: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:46:42: #1 total tags in treatment: 6142826 INFO @ Sat, 03 Apr 2021 09:46:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:46:42: #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 09:46:42: #1 tags after filtering in treatment: 5271664 INFO @ Sat, 03 Apr 2021 09:46:42: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 09:46:42: #1 finished! INFO @ Sat, 03 Apr 2021 09:46:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:46:42: #2 number of paired peaks: 732 WARNING @ Sat, 03 Apr 2021 09:46:42: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 03 Apr 2021 09:46:42: start model_add_line... INFO @ Sat, 03 Apr 2021 09:46:43: start X-correlation... INFO @ Sat, 03 Apr 2021 09:46:43: end of X-cor INFO @ Sat, 03 Apr 2021 09:46:43: #2 finished! INFO @ Sat, 03 Apr 2021 09:46:43: #2 predicted fragment length is 150 bps INFO @ Sat, 03 Apr 2021 09:46:43: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 03 Apr 2021 09:46:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.20_model.r WARNING @ Sat, 03 Apr 2021 09:46:43: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:46:43: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sat, 03 Apr 2021 09:46:43: #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 09:46:43: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:46:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:46:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:46:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806724/SRX7806724.20_summits.bed INFO @ Sat, 03 Apr 2021 09:46:59: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (438 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。