Job ID = 12265319 SRX = SRX5736450 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 35895308 spots for SRR8956861/SRR8956861.sra Written 35895308 spots for SRR8956861/SRR8956861.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265634 ("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: 00:45:23 35895308 reads; of these: 35895308 (100.00%) were paired; of these: 15438675 (43.01%) aligned concordantly 0 times 5924869 (16.51%) aligned concordantly exactly 1 time 14531764 (40.48%) aligned concordantly >1 times ---- 15438675 pairs aligned concordantly 0 times; of these: 461617 (2.99%) aligned discordantly 1 time ---- 14977058 pairs aligned 0 times concordantly or discordantly; of these: 29954116 mates make up the pairs; of these: 27840467 (92.94%) aligned 0 times 267955 (0.89%) aligned exactly 1 time 1845694 (6.16%) aligned >1 times 61.22% overall alignment rate Time searching: 00:45:23 Overall time: 00:45:23 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] 11896970 / 20789676 = 0.5723 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 07:33:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.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 07:33:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:33:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:33:40: 1000000 INFO @ Sat, 03 Apr 2021 07:33:48: 2000000 INFO @ Sat, 03 Apr 2021 07:33:56: 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 07:34:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.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 07:34:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:34:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:34:05: 4000000 INFO @ Sat, 03 Apr 2021 07:34:11: 1000000 INFO @ Sat, 03 Apr 2021 07:34:14: 5000000 INFO @ Sat, 03 Apr 2021 07:34:20: 2000000 INFO @ Sat, 03 Apr 2021 07:34:24: 6000000 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 07:34:30: 3000000 INFO @ Sat, 03 Apr 2021 07:34:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.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 07:34:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:34:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:34:33: 7000000 INFO @ Sat, 03 Apr 2021 07:34:39: 4000000 INFO @ Sat, 03 Apr 2021 07:34:41: 1000000 INFO @ Sat, 03 Apr 2021 07:34:43: 8000000 INFO @ Sat, 03 Apr 2021 07:34:49: 5000000 INFO @ Sat, 03 Apr 2021 07:34:50: 2000000 INFO @ Sat, 03 Apr 2021 07:34:52: 9000000 INFO @ Sat, 03 Apr 2021 07:34:59: 6000000 INFO @ Sat, 03 Apr 2021 07:34:59: 3000000 INFO @ Sat, 03 Apr 2021 07:35:02: 10000000 INFO @ Sat, 03 Apr 2021 07:35:08: 4000000 INFO @ Sat, 03 Apr 2021 07:35:08: 7000000 INFO @ Sat, 03 Apr 2021 07:35:11: 11000000 INFO @ Sat, 03 Apr 2021 07:35:17: 5000000 INFO @ Sat, 03 Apr 2021 07:35:18: 8000000 INFO @ Sat, 03 Apr 2021 07:35:21: 12000000 INFO @ Sat, 03 Apr 2021 07:35:26: 6000000 INFO @ Sat, 03 Apr 2021 07:35:28: 9000000 INFO @ Sat, 03 Apr 2021 07:35:30: 13000000 INFO @ Sat, 03 Apr 2021 07:35:35: 7000000 INFO @ Sat, 03 Apr 2021 07:35:37: 10000000 INFO @ Sat, 03 Apr 2021 07:35:40: 14000000 INFO @ Sat, 03 Apr 2021 07:35:44: 8000000 INFO @ Sat, 03 Apr 2021 07:35:47: 11000000 INFO @ Sat, 03 Apr 2021 07:35:49: 15000000 INFO @ Sat, 03 Apr 2021 07:35:53: 9000000 INFO @ Sat, 03 Apr 2021 07:35:56: 12000000 INFO @ Sat, 03 Apr 2021 07:35:59: 16000000 INFO @ Sat, 03 Apr 2021 07:36:03: 10000000 INFO @ Sat, 03 Apr 2021 07:36:05: 13000000 INFO @ Sat, 03 Apr 2021 07:36:08: 17000000 INFO @ Sat, 03 Apr 2021 07:36:11: 11000000 INFO @ Sat, 03 Apr 2021 07:36:15: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:36:18: 18000000 INFO @ Sat, 03 Apr 2021 07:36:20: 12000000 INFO @ Sat, 03 Apr 2021 07:36:24: 15000000 INFO @ Sat, 03 Apr 2021 07:36:28: 19000000 INFO @ Sat, 03 Apr 2021 07:36:29: 13000000 INFO @ Sat, 03 Apr 2021 07:36:34: 16000000 INFO @ Sat, 03 Apr 2021 07:36:38: 20000000 INFO @ Sat, 03 Apr 2021 07:36:38: 14000000 INFO @ Sat, 03 Apr 2021 07:36:39: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:36:39: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:36:39: #1 total tags in treatment: 8606624 INFO @ Sat, 03 Apr 2021 07:36:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:36:39: #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 07:36:39: #1 tags after filtering in treatment: 6406422 INFO @ Sat, 03 Apr 2021 07:36:39: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:36:39: #1 finished! INFO @ Sat, 03 Apr 2021 07:36:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:36:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:36:40: #2 number of paired peaks: 742 WARNING @ Sat, 03 Apr 2021 07:36:40: Fewer paired peaks (742) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 742 pairs to build model! INFO @ Sat, 03 Apr 2021 07:36:40: start model_add_line... INFO @ Sat, 03 Apr 2021 07:36:40: start X-correlation... INFO @ Sat, 03 Apr 2021 07:36:40: end of X-cor INFO @ Sat, 03 Apr 2021 07:36:40: #2 finished! INFO @ Sat, 03 Apr 2021 07:36:40: #2 predicted fragment length is 134 bps INFO @ Sat, 03 Apr 2021 07:36:40: #2 alternative fragment length(s) may be 134 bps INFO @ Sat, 03 Apr 2021 07:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.05_model.r WARNING @ Sat, 03 Apr 2021 07:36:40: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:36:40: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Sat, 03 Apr 2021 07:36:40: #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 07:36:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:36:43: 17000000 INFO @ Sat, 03 Apr 2021 07:36:46: 15000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:36:53: 18000000 INFO @ Sat, 03 Apr 2021 07:36:55: 16000000 INFO @ Sat, 03 Apr 2021 07:36:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:37:03: 19000000 INFO @ Sat, 03 Apr 2021 07:37:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.05_summits.bed INFO @ Sat, 03 Apr 2021 07:37:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3413 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:37:04: 17000000 INFO @ Sat, 03 Apr 2021 07:37:12: 20000000 INFO @ Sat, 03 Apr 2021 07:37:13: 18000000 INFO @ Sat, 03 Apr 2021 07:37:13: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:37:13: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:37:13: #1 total tags in treatment: 8606624 INFO @ Sat, 03 Apr 2021 07:37:13: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:37:13: #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 07:37:14: #1 tags after filtering in treatment: 6406422 INFO @ Sat, 03 Apr 2021 07:37:14: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:37:14: #1 finished! INFO @ Sat, 03 Apr 2021 07:37:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:37:14: #2 number of paired peaks: 742 WARNING @ Sat, 03 Apr 2021 07:37:14: Fewer paired peaks (742) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 742 pairs to build model! INFO @ Sat, 03 Apr 2021 07:37:14: start model_add_line... INFO @ Sat, 03 Apr 2021 07:37:14: start X-correlation... INFO @ Sat, 03 Apr 2021 07:37:14: end of X-cor INFO @ Sat, 03 Apr 2021 07:37:14: #2 finished! INFO @ Sat, 03 Apr 2021 07:37:14: #2 predicted fragment length is 134 bps INFO @ Sat, 03 Apr 2021 07:37:14: #2 alternative fragment length(s) may be 134 bps INFO @ Sat, 03 Apr 2021 07:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.10_model.r WARNING @ Sat, 03 Apr 2021 07:37:14: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:37:14: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Sat, 03 Apr 2021 07:37:14: #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 07:37:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:37:21: 19000000 INFO @ Sat, 03 Apr 2021 07:37:28: 20000000 INFO @ Sat, 03 Apr 2021 07:37:29: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:37:29: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:37:29: #1 total tags in treatment: 8606624 INFO @ Sat, 03 Apr 2021 07:37:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:37:29: #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 07:37:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:37:29: #1 tags after filtering in treatment: 6406422 INFO @ Sat, 03 Apr 2021 07:37:29: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:37:29: #1 finished! INFO @ Sat, 03 Apr 2021 07:37:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:37:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:37:30: #2 number of paired peaks: 742 WARNING @ Sat, 03 Apr 2021 07:37:30: Fewer paired peaks (742) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 742 pairs to build model! INFO @ Sat, 03 Apr 2021 07:37:30: start model_add_line... INFO @ Sat, 03 Apr 2021 07:37:30: start X-correlation... INFO @ Sat, 03 Apr 2021 07:37:30: end of X-cor INFO @ Sat, 03 Apr 2021 07:37:30: #2 finished! INFO @ Sat, 03 Apr 2021 07:37:30: #2 predicted fragment length is 134 bps INFO @ Sat, 03 Apr 2021 07:37:30: #2 alternative fragment length(s) may be 134 bps INFO @ Sat, 03 Apr 2021 07:37:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.20_model.r WARNING @ Sat, 03 Apr 2021 07:37:30: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:37:30: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Sat, 03 Apr 2021 07:37:30: #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 07:37:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:37:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.10_summits.bed INFO @ Sat, 03 Apr 2021 07:37:37: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1674 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:37:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:37:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736450/SRX5736450.20_summits.bed INFO @ Sat, 03 Apr 2021 07:37:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (755 records, 4 fields): 2 millis CompletedMACS2peakCalling