Job ID = 14167100 SRX = SRX10412062 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16826830 spots for SRR14035726/SRR14035726.sra Written 16826830 spots for SRR14035726/SRR14035726.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167754 ("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: 01:14:41 16826830 reads; of these: 16826830 (100.00%) were paired; of these: 1889718 (11.23%) aligned concordantly 0 times 10716167 (63.69%) aligned concordantly exactly 1 time 4220945 (25.08%) aligned concordantly >1 times ---- 1889718 pairs aligned concordantly 0 times; of these: 334981 (17.73%) aligned discordantly 1 time ---- 1554737 pairs aligned 0 times concordantly or discordantly; of these: 3109474 mates make up the pairs; of these: 2345453 (75.43%) aligned 0 times 262481 (8.44%) aligned exactly 1 time 501540 (16.13%) aligned >1 times 93.03% overall alignment rate Time searching: 01:14:41 Overall time: 01:14:41 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] 3420407 / 15228119 = 0.2246 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 @ Fri, 10 Dec 2021 11:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.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 @ Fri, 10 Dec 2021 11:19:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:19:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:19:41: 1000000 INFO @ Fri, 10 Dec 2021 11:19:49: 2000000 INFO @ Fri, 10 Dec 2021 11:19:57: 3000000 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 @ Fri, 10 Dec 2021 11:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.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 @ Fri, 10 Dec 2021 11:20:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:20:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:20:05: 4000000 INFO @ Fri, 10 Dec 2021 11:20:12: 1000000 INFO @ Fri, 10 Dec 2021 11:20:15: 5000000 INFO @ Fri, 10 Dec 2021 11:20:21: 2000000 INFO @ Fri, 10 Dec 2021 11:20:24: 6000000 INFO @ Fri, 10 Dec 2021 11:20:30: 3000000 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 @ Fri, 10 Dec 2021 11:20:33: 7000000 INFO @ Fri, 10 Dec 2021 11:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.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 @ Fri, 10 Dec 2021 11:20:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:20:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:20:39: 4000000 INFO @ Fri, 10 Dec 2021 11:20:43: 8000000 INFO @ Fri, 10 Dec 2021 11:20:43: 1000000 INFO @ Fri, 10 Dec 2021 11:20:49: 5000000 INFO @ Fri, 10 Dec 2021 11:20:52: 9000000 INFO @ Fri, 10 Dec 2021 11:20:52: 2000000 INFO @ Fri, 10 Dec 2021 11:20:58: 6000000 INFO @ Fri, 10 Dec 2021 11:21:02: 10000000 INFO @ Fri, 10 Dec 2021 11:21:02: 3000000 INFO @ Fri, 10 Dec 2021 11:21:07: 7000000 INFO @ Fri, 10 Dec 2021 11:21:11: 11000000 INFO @ Fri, 10 Dec 2021 11:21:12: 4000000 INFO @ Fri, 10 Dec 2021 11:21:16: 8000000 INFO @ Fri, 10 Dec 2021 11:21:21: 12000000 INFO @ Fri, 10 Dec 2021 11:21:21: 5000000 INFO @ Fri, 10 Dec 2021 11:21:25: 9000000 INFO @ Fri, 10 Dec 2021 11:21:31: 13000000 INFO @ Fri, 10 Dec 2021 11:21:31: 6000000 INFO @ Fri, 10 Dec 2021 11:21:34: 10000000 INFO @ Fri, 10 Dec 2021 11:21:40: 14000000 INFO @ Fri, 10 Dec 2021 11:21:41: 7000000 INFO @ Fri, 10 Dec 2021 11:21:43: 11000000 INFO @ Fri, 10 Dec 2021 11:21:50: 15000000 INFO @ Fri, 10 Dec 2021 11:21:50: 8000000 INFO @ Fri, 10 Dec 2021 11:21:53: 12000000 INFO @ Fri, 10 Dec 2021 11:21:59: 16000000 INFO @ Fri, 10 Dec 2021 11:21:59: 9000000 INFO @ Fri, 10 Dec 2021 11:22:02: 13000000 INFO @ Fri, 10 Dec 2021 11:22:08: 17000000 INFO @ Fri, 10 Dec 2021 11:22:09: 10000000 INFO @ Fri, 10 Dec 2021 11:22:11: 14000000 INFO @ Fri, 10 Dec 2021 11:22:19: 18000000 INFO @ Fri, 10 Dec 2021 11:22:19: 11000000 INFO @ Fri, 10 Dec 2021 11:22:20: 15000000 INFO @ Fri, 10 Dec 2021 11:22:29: 19000000 INFO @ Fri, 10 Dec 2021 11:22:29: 12000000 INFO @ Fri, 10 Dec 2021 11:22:29: 16000000 INFO @ Fri, 10 Dec 2021 11:22:38: 17000000 INFO @ Fri, 10 Dec 2021 11:22:39: 20000000 INFO @ Fri, 10 Dec 2021 11:22:39: 13000000 INFO @ Fri, 10 Dec 2021 11:22:47: 18000000 INFO @ Fri, 10 Dec 2021 11:22:49: 14000000 INFO @ Fri, 10 Dec 2021 11:22:49: 21000000 INFO @ Fri, 10 Dec 2021 11:22:57: 19000000 INFO @ Fri, 10 Dec 2021 11:22:58: 15000000 INFO @ Fri, 10 Dec 2021 11:22:58: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:23:06: 20000000 INFO @ Fri, 10 Dec 2021 11:23:07: 16000000 INFO @ Fri, 10 Dec 2021 11:23:08: 23000000 INFO @ Fri, 10 Dec 2021 11:23:15: 21000000 INFO @ Fri, 10 Dec 2021 11:23:17: 17000000 INFO @ Fri, 10 Dec 2021 11:23:17: 24000000 INFO @ Fri, 10 Dec 2021 11:23:21: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:23:21: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:23:21: #1 total tags in treatment: 11572176 INFO @ Fri, 10 Dec 2021 11:23:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:23:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:23:22: #1 tags after filtering in treatment: 10807725 INFO @ Fri, 10 Dec 2021 11:23:22: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 11:23:22: #1 finished! INFO @ Fri, 10 Dec 2021 11:23:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:23:22: #2 number of paired peaks: 400 WARNING @ Fri, 10 Dec 2021 11:23:22: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 10 Dec 2021 11:23:22: start model_add_line... INFO @ Fri, 10 Dec 2021 11:23:23: start X-correlation... INFO @ Fri, 10 Dec 2021 11:23:23: end of X-cor INFO @ Fri, 10 Dec 2021 11:23:23: #2 finished! INFO @ Fri, 10 Dec 2021 11:23:23: #2 predicted fragment length is 196 bps INFO @ Fri, 10 Dec 2021 11:23:23: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 10 Dec 2021 11:23:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.05_model.r WARNING @ Fri, 10 Dec 2021 11:23:23: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:23:23: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Fri, 10 Dec 2021 11:23:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:23:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:23:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:23:24: 22000000 INFO @ Fri, 10 Dec 2021 11:23:26: 18000000 INFO @ Fri, 10 Dec 2021 11:23:33: 23000000 INFO @ Fri, 10 Dec 2021 11:23:35: 19000000 INFO @ Fri, 10 Dec 2021 11:23:42: 24000000 INFO @ Fri, 10 Dec 2021 11:23:44: 20000000 INFO @ Fri, 10 Dec 2021 11:23:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:23:46: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:23:46: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:23:46: #1 total tags in treatment: 11572176 INFO @ Fri, 10 Dec 2021 11:23:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:23:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:23:47: #1 tags after filtering in treatment: 10807725 INFO @ Fri, 10 Dec 2021 11:23:47: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 11:23:47: #1 finished! INFO @ Fri, 10 Dec 2021 11:23:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:23:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:23:47: #2 number of paired peaks: 400 WARNING @ Fri, 10 Dec 2021 11:23:47: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 10 Dec 2021 11:23:47: start model_add_line... INFO @ Fri, 10 Dec 2021 11:23:48: start X-correlation... INFO @ Fri, 10 Dec 2021 11:23:48: end of X-cor INFO @ Fri, 10 Dec 2021 11:23:48: #2 finished! INFO @ Fri, 10 Dec 2021 11:23:48: #2 predicted fragment length is 196 bps INFO @ Fri, 10 Dec 2021 11:23:48: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 10 Dec 2021 11:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.10_model.r WARNING @ Fri, 10 Dec 2021 11:23:48: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:23:48: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Fri, 10 Dec 2021 11:23:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:23:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:23:52: 21000000 INFO @ Fri, 10 Dec 2021 11:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:23:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.05_summits.bed INFO @ Fri, 10 Dec 2021 11:23:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8076 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:24:00: 22000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:24:08: 23000000 INFO @ Fri, 10 Dec 2021 11:24:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:24:16: 24000000 INFO @ Fri, 10 Dec 2021 11:24:20: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:24:20: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:24:20: #1 total tags in treatment: 11572176 INFO @ Fri, 10 Dec 2021 11:24:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:24:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:24:20: #1 tags after filtering in treatment: 10807725 INFO @ Fri, 10 Dec 2021 11:24:20: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 11:24:20: #1 finished! INFO @ Fri, 10 Dec 2021 11:24:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:24:21: #2 number of paired peaks: 400 WARNING @ Fri, 10 Dec 2021 11:24:21: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 10 Dec 2021 11:24:21: start model_add_line... INFO @ Fri, 10 Dec 2021 11:24:21: start X-correlation... INFO @ Fri, 10 Dec 2021 11:24:21: end of X-cor INFO @ Fri, 10 Dec 2021 11:24:21: #2 finished! INFO @ Fri, 10 Dec 2021 11:24:21: #2 predicted fragment length is 196 bps INFO @ Fri, 10 Dec 2021 11:24:21: #2 alternative fragment length(s) may be 196 bps INFO @ Fri, 10 Dec 2021 11:24:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.20_model.r WARNING @ Fri, 10 Dec 2021 11:24:21: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:24:21: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Fri, 10 Dec 2021 11:24:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:24:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:24:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:24:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:24:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:24:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.10_summits.bed INFO @ Fri, 10 Dec 2021 11:24:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4541 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:24:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:24:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:24:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412062/SRX10412062.20_summits.bed INFO @ Fri, 10 Dec 2021 11:24:56: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1524 records, 4 fields): 4 millis CompletedMACS2peakCalling