Job ID = 14171653 SRX = SRX10386215 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20666476 spots for SRR14009280/SRR14009280.sra Written 20666476 spots for SRR14009280/SRR14009280.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172411 ("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: 01:17:15 20666476 reads; of these: 20666476 (100.00%) were paired; of these: 2427885 (11.75%) aligned concordantly 0 times 9655890 (46.72%) aligned concordantly exactly 1 time 8582701 (41.53%) aligned concordantly >1 times ---- 2427885 pairs aligned concordantly 0 times; of these: 305864 (12.60%) aligned discordantly 1 time ---- 2122021 pairs aligned 0 times concordantly or discordantly; of these: 4244042 mates make up the pairs; of these: 3340993 (78.72%) aligned 0 times 394382 (9.29%) aligned exactly 1 time 508667 (11.99%) aligned >1 times 91.92% overall alignment rate Time searching: 01:17:15 Overall time: 01:17:15 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] 4724049 / 18485790 = 0.2556 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 13:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.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 13:46:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:46:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:46:12: 1000000 INFO @ Sat, 11 Dec 2021 13:46:19: 2000000 INFO @ Sat, 11 Dec 2021 13:46:26: 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 @ Sat, 11 Dec 2021 13:46:34: 4000000 INFO @ Sat, 11 Dec 2021 13:46:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.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 13:46:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:46:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:46:41: 5000000 INFO @ Sat, 11 Dec 2021 13:46:43: 1000000 INFO @ Sat, 11 Dec 2021 13:46:49: 6000000 INFO @ Sat, 11 Dec 2021 13:46:50: 2000000 INFO @ Sat, 11 Dec 2021 13:46:56: 7000000 INFO @ Sat, 11 Dec 2021 13:46:58: 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 @ Sat, 11 Dec 2021 13:47:04: 8000000 INFO @ Sat, 11 Dec 2021 13:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.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 13:47:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:47:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:47:05: 4000000 INFO @ Sat, 11 Dec 2021 13:47:11: 9000000 INFO @ Sat, 11 Dec 2021 13:47:12: 1000000 INFO @ Sat, 11 Dec 2021 13:47:13: 5000000 INFO @ Sat, 11 Dec 2021 13:47:19: 10000000 INFO @ Sat, 11 Dec 2021 13:47:19: 2000000 INFO @ Sat, 11 Dec 2021 13:47:20: 6000000 INFO @ Sat, 11 Dec 2021 13:47:26: 3000000 INFO @ Sat, 11 Dec 2021 13:47:27: 11000000 INFO @ Sat, 11 Dec 2021 13:47:28: 7000000 INFO @ Sat, 11 Dec 2021 13:47:33: 4000000 INFO @ Sat, 11 Dec 2021 13:47:34: 12000000 INFO @ Sat, 11 Dec 2021 13:47:36: 8000000 INFO @ Sat, 11 Dec 2021 13:47:40: 5000000 INFO @ Sat, 11 Dec 2021 13:47:42: 13000000 INFO @ Sat, 11 Dec 2021 13:47:43: 9000000 INFO @ Sat, 11 Dec 2021 13:47:47: 6000000 INFO @ Sat, 11 Dec 2021 13:47:50: 14000000 INFO @ Sat, 11 Dec 2021 13:47:51: 10000000 INFO @ Sat, 11 Dec 2021 13:47:54: 7000000 INFO @ Sat, 11 Dec 2021 13:47:57: 15000000 INFO @ Sat, 11 Dec 2021 13:47:59: 11000000 INFO @ Sat, 11 Dec 2021 13:48:01: 8000000 INFO @ Sat, 11 Dec 2021 13:48:05: 16000000 INFO @ Sat, 11 Dec 2021 13:48:06: 12000000 INFO @ Sat, 11 Dec 2021 13:48:08: 9000000 INFO @ Sat, 11 Dec 2021 13:48:13: 17000000 INFO @ Sat, 11 Dec 2021 13:48:14: 13000000 INFO @ Sat, 11 Dec 2021 13:48:15: 10000000 INFO @ Sat, 11 Dec 2021 13:48:20: 18000000 INFO @ Sat, 11 Dec 2021 13:48:22: 14000000 INFO @ Sat, 11 Dec 2021 13:48:22: 11000000 INFO @ Sat, 11 Dec 2021 13:48:28: 19000000 INFO @ Sat, 11 Dec 2021 13:48:29: 12000000 INFO @ Sat, 11 Dec 2021 13:48:29: 15000000 INFO @ Sat, 11 Dec 2021 13:48:36: 13000000 INFO @ Sat, 11 Dec 2021 13:48:36: 20000000 INFO @ Sat, 11 Dec 2021 13:48:37: 16000000 INFO @ Sat, 11 Dec 2021 13:48:43: 14000000 INFO @ Sat, 11 Dec 2021 13:48:43: 21000000 INFO @ Sat, 11 Dec 2021 13:48:45: 17000000 INFO @ Sat, 11 Dec 2021 13:48:50: 15000000 INFO @ Sat, 11 Dec 2021 13:48:51: 22000000 INFO @ Sat, 11 Dec 2021 13:48:52: 18000000 INFO @ Sat, 11 Dec 2021 13:48:57: 16000000 INFO @ Sat, 11 Dec 2021 13:48:59: 23000000 INFO @ Sat, 11 Dec 2021 13:49:00: 19000000 INFO @ Sat, 11 Dec 2021 13:49:04: 17000000 INFO @ Sat, 11 Dec 2021 13:49:06: 24000000 INFO @ Sat, 11 Dec 2021 13:49:08: 20000000 INFO @ Sat, 11 Dec 2021 13:49:11: 18000000 INFO @ Sat, 11 Dec 2021 13:49:14: 25000000 INFO @ Sat, 11 Dec 2021 13:49:15: 21000000 INFO @ Sat, 11 Dec 2021 13:49:17: 19000000 INFO @ Sat, 11 Dec 2021 13:49:21: 26000000 INFO @ Sat, 11 Dec 2021 13:49:23: 22000000 INFO @ Sat, 11 Dec 2021 13:49:25: 20000000 INFO @ Sat, 11 Dec 2021 13:49:29: 27000000 INFO @ Sat, 11 Dec 2021 13:49:30: 23000000 INFO @ Sat, 11 Dec 2021 13:49:32: 21000000 INFO @ Sat, 11 Dec 2021 13:49:37: 28000000 INFO @ Sat, 11 Dec 2021 13:49:38: 24000000 INFO @ Sat, 11 Dec 2021 13:49:39: 22000000 INFO @ Sat, 11 Dec 2021 13:49:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:49:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:49:41: #1 total tags in treatment: 13527314 INFO @ Sat, 11 Dec 2021 13:49:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:49:41: #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 13:49:41: #1 tags after filtering in treatment: 10394266 INFO @ Sat, 11 Dec 2021 13:49:41: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 13:49:41: #1 finished! INFO @ Sat, 11 Dec 2021 13:49:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:49:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:49:42: #2 number of paired peaks: 520 WARNING @ Sat, 11 Dec 2021 13:49:42: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Sat, 11 Dec 2021 13:49:42: start model_add_line... INFO @ Sat, 11 Dec 2021 13:49:42: start X-correlation... INFO @ Sat, 11 Dec 2021 13:49:42: end of X-cor INFO @ Sat, 11 Dec 2021 13:49:42: #2 finished! INFO @ Sat, 11 Dec 2021 13:49:42: #2 predicted fragment length is 93 bps INFO @ Sat, 11 Dec 2021 13:49:42: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 11 Dec 2021 13:49:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.05_model.r WARNING @ Sat, 11 Dec 2021 13:49:42: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:49:42: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 11 Dec 2021 13:49:42: #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 13:49:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:49:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:49:45: 23000000 INFO @ Sat, 11 Dec 2021 13:49:46: 25000000 INFO @ Sat, 11 Dec 2021 13:49:52: 24000000 INFO @ Sat, 11 Dec 2021 13:49:53: 26000000 INFO @ Sat, 11 Dec 2021 13:49:59: 25000000 INFO @ Sat, 11 Dec 2021 13:50:01: 27000000 INFO @ Sat, 11 Dec 2021 13:50:06: 26000000 INFO @ Sat, 11 Dec 2021 13:50:08: 28000000 INFO @ Sat, 11 Dec 2021 13:50:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:50:13: 27000000 INFO @ Sat, 11 Dec 2021 13:50:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:50:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:50:13: #1 total tags in treatment: 13527314 INFO @ Sat, 11 Dec 2021 13:50:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:50:13: #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 13:50:13: #1 tags after filtering in treatment: 10394266 INFO @ Sat, 11 Dec 2021 13:50:13: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 13:50:13: #1 finished! INFO @ Sat, 11 Dec 2021 13:50:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:50:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:50:14: #2 number of paired peaks: 520 WARNING @ Sat, 11 Dec 2021 13:50:14: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Sat, 11 Dec 2021 13:50:14: start model_add_line... INFO @ Sat, 11 Dec 2021 13:50:14: start X-correlation... INFO @ Sat, 11 Dec 2021 13:50:14: end of X-cor INFO @ Sat, 11 Dec 2021 13:50:14: #2 finished! INFO @ Sat, 11 Dec 2021 13:50:14: #2 predicted fragment length is 93 bps INFO @ Sat, 11 Dec 2021 13:50:14: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 11 Dec 2021 13:50:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.10_model.r WARNING @ Sat, 11 Dec 2021 13:50:14: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:50:14: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 11 Dec 2021 13:50:14: #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 13:50:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:50:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:50:19: 28000000 INFO @ Sat, 11 Dec 2021 13:50:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:50:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:50:23: #1 total tags in treatment: 13527314 INFO @ Sat, 11 Dec 2021 13:50:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:50:23: #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 13:50:23: #1 tags after filtering in treatment: 10394266 INFO @ Sat, 11 Dec 2021 13:50:23: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 11 Dec 2021 13:50:23: #1 finished! INFO @ Sat, 11 Dec 2021 13:50:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:50:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:50:24: #2 number of paired peaks: 520 WARNING @ Sat, 11 Dec 2021 13:50:24: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Sat, 11 Dec 2021 13:50:24: start model_add_line... INFO @ Sat, 11 Dec 2021 13:50:24: start X-correlation... INFO @ Sat, 11 Dec 2021 13:50:24: end of X-cor INFO @ Sat, 11 Dec 2021 13:50:24: #2 finished! INFO @ Sat, 11 Dec 2021 13:50:24: #2 predicted fragment length is 93 bps INFO @ Sat, 11 Dec 2021 13:50:24: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 11 Dec 2021 13:50:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.20_model.r WARNING @ Sat, 11 Dec 2021 13:50:24: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:50:24: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 11 Dec 2021 13:50:24: #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 13:50:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:50:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:50:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:50:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:50:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.05_summits.bed INFO @ Sat, 11 Dec 2021 13:50:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1703 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:50:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:50:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:50:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:50:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:50:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.10_summits.bed INFO @ Sat, 11 Dec 2021 13:50:57: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1278 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386215/SRX10386215.20_summits.bed INFO @ Sat, 11 Dec 2021 13:51:07: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (865 records, 4 fields): 3 millis CompletedMACS2peakCalling