Job ID = 14171634 SRX = SRX10386211 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23275185 spots for SRR14009276/SRR14009276.sra Written 23275185 spots for SRR14009276/SRR14009276.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172189 ("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: 00:33:55 23275185 reads; of these: 23275185 (100.00%) were paired; of these: 6642428 (28.54%) aligned concordantly 0 times 11490267 (49.37%) aligned concordantly exactly 1 time 5142490 (22.09%) aligned concordantly >1 times ---- 6642428 pairs aligned concordantly 0 times; of these: 812991 (12.24%) aligned discordantly 1 time ---- 5829437 pairs aligned 0 times concordantly or discordantly; of these: 11658874 mates make up the pairs; of these: 10490804 (89.98%) aligned 0 times 472804 (4.06%) aligned exactly 1 time 695266 (5.96%) aligned >1 times 77.46% overall alignment rate Time searching: 00:33:55 Overall time: 00:33:55 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 16 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] 2428343 / 17349553 = 0.1400 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 12:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.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 12:57:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:57:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:57:08: 1000000 INFO @ Sat, 11 Dec 2021 12:57:13: 2000000 INFO @ Sat, 11 Dec 2021 12:57:18: 3000000 INFO @ Sat, 11 Dec 2021 12:57:23: 4000000 INFO @ Sat, 11 Dec 2021 12:57:28: 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 12:57:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.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 12:57:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:57:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:57:34: 6000000 INFO @ Sat, 11 Dec 2021 12:57:40: 1000000 INFO @ Sat, 11 Dec 2021 12:57:40: 7000000 INFO @ Sat, 11 Dec 2021 12:57:47: 8000000 INFO @ Sat, 11 Dec 2021 12:57:47: 2000000 INFO @ Sat, 11 Dec 2021 12:57:53: 9000000 INFO @ Sat, 11 Dec 2021 12:57:54: 3000000 INFO @ Sat, 11 Dec 2021 12:58:00: 10000000 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 12:58:01: 4000000 INFO @ Sat, 11 Dec 2021 12:58:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.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 12:58:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:58:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:58:06: 11000000 INFO @ Sat, 11 Dec 2021 12:58:08: 5000000 INFO @ Sat, 11 Dec 2021 12:58:09: 1000000 INFO @ Sat, 11 Dec 2021 12:58:13: 12000000 INFO @ Sat, 11 Dec 2021 12:58:15: 6000000 INFO @ Sat, 11 Dec 2021 12:58:16: 2000000 INFO @ Sat, 11 Dec 2021 12:58:20: 13000000 INFO @ Sat, 11 Dec 2021 12:58:22: 7000000 INFO @ Sat, 11 Dec 2021 12:58:23: 3000000 INFO @ Sat, 11 Dec 2021 12:58:26: 14000000 INFO @ Sat, 11 Dec 2021 12:58:29: 8000000 INFO @ Sat, 11 Dec 2021 12:58:29: 4000000 INFO @ Sat, 11 Dec 2021 12:58:33: 15000000 INFO @ Sat, 11 Dec 2021 12:58:36: 5000000 INFO @ Sat, 11 Dec 2021 12:58:36: 9000000 INFO @ Sat, 11 Dec 2021 12:58:40: 16000000 INFO @ Sat, 11 Dec 2021 12:58:43: 6000000 INFO @ Sat, 11 Dec 2021 12:58:43: 10000000 INFO @ Sat, 11 Dec 2021 12:58:46: 17000000 INFO @ Sat, 11 Dec 2021 12:58:49: 7000000 INFO @ Sat, 11 Dec 2021 12:58:50: 11000000 INFO @ Sat, 11 Dec 2021 12:58:53: 18000000 INFO @ Sat, 11 Dec 2021 12:58:56: 8000000 INFO @ Sat, 11 Dec 2021 12:58:57: 12000000 INFO @ Sat, 11 Dec 2021 12:59:00: 19000000 INFO @ Sat, 11 Dec 2021 12:59:03: 9000000 INFO @ Sat, 11 Dec 2021 12:59:04: 13000000 INFO @ Sat, 11 Dec 2021 12:59:06: 20000000 INFO @ Sat, 11 Dec 2021 12:59:09: 10000000 INFO @ Sat, 11 Dec 2021 12:59:11: 14000000 INFO @ Sat, 11 Dec 2021 12:59:13: 21000000 INFO @ Sat, 11 Dec 2021 12:59:16: 11000000 INFO @ Sat, 11 Dec 2021 12:59:18: 15000000 INFO @ Sat, 11 Dec 2021 12:59:20: 22000000 INFO @ Sat, 11 Dec 2021 12:59:23: 12000000 INFO @ Sat, 11 Dec 2021 12:59:25: 16000000 INFO @ Sat, 11 Dec 2021 12:59:27: 23000000 INFO @ Sat, 11 Dec 2021 12:59:29: 13000000 INFO @ Sat, 11 Dec 2021 12:59:32: 17000000 INFO @ Sat, 11 Dec 2021 12:59:33: 24000000 INFO @ Sat, 11 Dec 2021 12:59:36: 14000000 INFO @ Sat, 11 Dec 2021 12:59:39: 18000000 INFO @ Sat, 11 Dec 2021 12:59:40: 25000000 INFO @ Sat, 11 Dec 2021 12:59:43: 15000000 INFO @ Sat, 11 Dec 2021 12:59:46: 19000000 INFO @ Sat, 11 Dec 2021 12:59:47: 26000000 INFO @ Sat, 11 Dec 2021 12:59:49: 16000000 INFO @ Sat, 11 Dec 2021 12:59:53: 20000000 INFO @ Sat, 11 Dec 2021 12:59:54: 27000000 INFO @ Sat, 11 Dec 2021 12:59:56: 17000000 INFO @ Sat, 11 Dec 2021 13:00:00: 28000000 INFO @ Sat, 11 Dec 2021 13:00:01: 21000000 INFO @ Sat, 11 Dec 2021 13:00:03: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:00:07: 29000000 INFO @ Sat, 11 Dec 2021 13:00:08: 22000000 INFO @ Sat, 11 Dec 2021 13:00:09: 19000000 INFO @ Sat, 11 Dec 2021 13:00:14: 30000000 INFO @ Sat, 11 Dec 2021 13:00:15: 23000000 INFO @ Sat, 11 Dec 2021 13:00:16: 20000000 INFO @ Sat, 11 Dec 2021 13:00:20: 31000000 INFO @ Sat, 11 Dec 2021 13:00:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:00:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:00:22: #1 total tags in treatment: 14263208 INFO @ Sat, 11 Dec 2021 13:00:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:00:22: #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 13:00:22: #1 tags after filtering in treatment: 12529950 INFO @ Sat, 11 Dec 2021 13:00:22: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 13:00:22: #1 finished! INFO @ Sat, 11 Dec 2021 13:00:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:00:22: 24000000 INFO @ Sat, 11 Dec 2021 13:00:23: 21000000 INFO @ Sat, 11 Dec 2021 13:00:23: #2 number of paired peaks: 179 WARNING @ Sat, 11 Dec 2021 13:00:23: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 11 Dec 2021 13:00:23: start model_add_line... INFO @ Sat, 11 Dec 2021 13:00:23: start X-correlation... INFO @ Sat, 11 Dec 2021 13:00:23: end of X-cor INFO @ Sat, 11 Dec 2021 13:00:23: #2 finished! INFO @ Sat, 11 Dec 2021 13:00:23: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 13:00:23: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 13:00:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.05_model.r WARNING @ Sat, 11 Dec 2021 13:00:23: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:00:23: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 13:00:23: #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 13:00:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:00:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:00:29: 22000000 INFO @ Sat, 11 Dec 2021 13:00:29: 25000000 INFO @ Sat, 11 Dec 2021 13:00:36: 23000000 INFO @ Sat, 11 Dec 2021 13:00:36: 26000000 INFO @ Sat, 11 Dec 2021 13:00:42: 24000000 INFO @ Sat, 11 Dec 2021 13:00:44: 27000000 INFO @ Sat, 11 Dec 2021 13:00:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:00:49: 25000000 INFO @ Sat, 11 Dec 2021 13:00:51: 28000000 INFO @ Sat, 11 Dec 2021 13:00:56: 26000000 INFO @ Sat, 11 Dec 2021 13:00:58: 29000000 INFO @ Sat, 11 Dec 2021 13:00:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:00:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:00:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.05_summits.bed INFO @ Sat, 11 Dec 2021 13:00:58: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1539 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:01:02: 27000000 INFO @ Sat, 11 Dec 2021 13:01:05: 30000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:01:09: 28000000 INFO @ Sat, 11 Dec 2021 13:01:12: 31000000 INFO @ Sat, 11 Dec 2021 13:01:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:01:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:01:13: #1 total tags in treatment: 14263208 INFO @ Sat, 11 Dec 2021 13:01:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:01:13: #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 13:01:13: #1 tags after filtering in treatment: 12529950 INFO @ Sat, 11 Dec 2021 13:01:13: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 13:01:13: #1 finished! INFO @ Sat, 11 Dec 2021 13:01:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:01:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:01:14: #2 number of paired peaks: 179 WARNING @ Sat, 11 Dec 2021 13:01:14: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 11 Dec 2021 13:01:14: start model_add_line... INFO @ Sat, 11 Dec 2021 13:01:14: start X-correlation... INFO @ Sat, 11 Dec 2021 13:01:14: end of X-cor INFO @ Sat, 11 Dec 2021 13:01:14: #2 finished! INFO @ Sat, 11 Dec 2021 13:01:14: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 13:01:14: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 13:01:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.10_model.r WARNING @ Sat, 11 Dec 2021 13:01:14: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:01:14: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 13:01:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:01:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:01:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:01:15: 29000000 INFO @ Sat, 11 Dec 2021 13:01:21: 30000000 INFO @ Sat, 11 Dec 2021 13:01:26: 31000000 INFO @ Sat, 11 Dec 2021 13:01:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:01:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:01:27: #1 total tags in treatment: 14263208 INFO @ Sat, 11 Dec 2021 13:01:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:01:27: #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 13:01:27: #1 tags after filtering in treatment: 12529950 INFO @ Sat, 11 Dec 2021 13:01:27: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 11 Dec 2021 13:01:27: #1 finished! INFO @ Sat, 11 Dec 2021 13:01:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:01:28: #2 number of paired peaks: 179 WARNING @ Sat, 11 Dec 2021 13:01:28: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 11 Dec 2021 13:01:28: start model_add_line... INFO @ Sat, 11 Dec 2021 13:01:28: start X-correlation... INFO @ Sat, 11 Dec 2021 13:01:28: end of X-cor INFO @ Sat, 11 Dec 2021 13:01:28: #2 finished! INFO @ Sat, 11 Dec 2021 13:01:28: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 13:01:28: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 13:01:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.20_model.r WARNING @ Sat, 11 Dec 2021 13:01:28: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:01:28: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 13:01:28: #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 13:01:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:01:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.10_summits.bed INFO @ Sat, 11 Dec 2021 13:01:50: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1049 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:01:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:02:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:02:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:02:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386211/SRX10386211.20_summits.bed INFO @ Sat, 11 Dec 2021 13:02:03: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (693 records, 4 fields): 2 millis CompletedMACS2peakCalling