Job ID = 12265241 SRX = SRX4664620 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25125711 spots for SRR7813047/SRR7813047.sra Written 25125711 spots for SRR7813047/SRR7813047.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265553 ("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: 00:46:36 25125711 reads; of these: 25125711 (100.00%) were paired; of these: 7780687 (30.97%) aligned concordantly 0 times 9574279 (38.11%) aligned concordantly exactly 1 time 7770745 (30.93%) aligned concordantly >1 times ---- 7780687 pairs aligned concordantly 0 times; of these: 2636048 (33.88%) aligned discordantly 1 time ---- 5144639 pairs aligned 0 times concordantly or discordantly; of these: 10289278 mates make up the pairs; of these: 6844778 (66.52%) aligned 0 times 982627 (9.55%) aligned exactly 1 time 2461873 (23.93%) aligned >1 times 86.38% overall alignment rate Time searching: 00:46:36 Overall time: 00:46:36 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] 4525589 / 19655630 = 0.2302 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 07:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.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 07:17:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:17:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:17:48: 1000000 INFO @ Sat, 03 Apr 2021 07:17:54: 2000000 INFO @ Sat, 03 Apr 2021 07:18:00: 3000000 INFO @ Sat, 03 Apr 2021 07:18:06: 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 07:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.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 07:18:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:18:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:18:13: 5000000 INFO @ Sat, 03 Apr 2021 07:18:19: 1000000 INFO @ Sat, 03 Apr 2021 07:18:19: 6000000 INFO @ Sat, 03 Apr 2021 07:18:25: 7000000 INFO @ Sat, 03 Apr 2021 07:18:27: 2000000 INFO @ Sat, 03 Apr 2021 07:18:32: 8000000 INFO @ Sat, 03 Apr 2021 07:18:34: 3000000 INFO @ Sat, 03 Apr 2021 07:18:38: 9000000 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 07:18:41: 4000000 INFO @ Sat, 03 Apr 2021 07:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.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 07:18:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:18:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:18:44: 10000000 INFO @ Sat, 03 Apr 2021 07:18:48: 5000000 INFO @ Sat, 03 Apr 2021 07:18:49: 1000000 INFO @ Sat, 03 Apr 2021 07:18:51: 11000000 INFO @ Sat, 03 Apr 2021 07:18:55: 2000000 INFO @ Sat, 03 Apr 2021 07:18:56: 6000000 INFO @ Sat, 03 Apr 2021 07:18:57: 12000000 INFO @ Sat, 03 Apr 2021 07:19:02: 3000000 INFO @ Sat, 03 Apr 2021 07:19:03: 7000000 INFO @ Sat, 03 Apr 2021 07:19:04: 13000000 INFO @ Sat, 03 Apr 2021 07:19:09: 4000000 INFO @ Sat, 03 Apr 2021 07:19:10: 14000000 INFO @ Sat, 03 Apr 2021 07:19:10: 8000000 INFO @ Sat, 03 Apr 2021 07:19:16: 5000000 INFO @ Sat, 03 Apr 2021 07:19:17: 15000000 INFO @ Sat, 03 Apr 2021 07:19:18: 9000000 INFO @ Sat, 03 Apr 2021 07:19:23: 6000000 INFO @ Sat, 03 Apr 2021 07:19:24: 16000000 INFO @ Sat, 03 Apr 2021 07:19:25: 10000000 INFO @ Sat, 03 Apr 2021 07:19:30: 7000000 INFO @ Sat, 03 Apr 2021 07:19:31: 17000000 INFO @ Sat, 03 Apr 2021 07:19:33: 11000000 INFO @ Sat, 03 Apr 2021 07:19:36: 8000000 INFO @ Sat, 03 Apr 2021 07:19:37: 18000000 INFO @ Sat, 03 Apr 2021 07:19:40: 12000000 INFO @ Sat, 03 Apr 2021 07:19:43: 9000000 INFO @ Sat, 03 Apr 2021 07:19:44: 19000000 INFO @ Sat, 03 Apr 2021 07:19:47: 13000000 INFO @ Sat, 03 Apr 2021 07:19:49: 10000000 INFO @ Sat, 03 Apr 2021 07:19:50: 20000000 INFO @ Sat, 03 Apr 2021 07:19:55: 14000000 INFO @ Sat, 03 Apr 2021 07:19:56: 11000000 INFO @ Sat, 03 Apr 2021 07:19:57: 21000000 INFO @ Sat, 03 Apr 2021 07:20:03: 12000000 INFO @ Sat, 03 Apr 2021 07:20:03: 22000000 INFO @ Sat, 03 Apr 2021 07:20:03: 15000000 INFO @ Sat, 03 Apr 2021 07:20:09: 23000000 INFO @ Sat, 03 Apr 2021 07:20:09: 13000000 INFO @ Sat, 03 Apr 2021 07:20:11: 16000000 INFO @ Sat, 03 Apr 2021 07:20:16: 24000000 INFO @ Sat, 03 Apr 2021 07:20:16: 14000000 INFO @ Sat, 03 Apr 2021 07:20:19: 17000000 INFO @ Sat, 03 Apr 2021 07:20:22: 25000000 INFO @ Sat, 03 Apr 2021 07:20:23: 15000000 INFO @ Sat, 03 Apr 2021 07:20:26: 18000000 INFO @ Sat, 03 Apr 2021 07:20:28: 26000000 INFO @ Sat, 03 Apr 2021 07:20:29: 16000000 INFO @ Sat, 03 Apr 2021 07:20:33: 19000000 INFO @ Sat, 03 Apr 2021 07:20:35: 27000000 INFO @ Sat, 03 Apr 2021 07:20:36: 17000000 INFO @ Sat, 03 Apr 2021 07:20:41: 20000000 INFO @ Sat, 03 Apr 2021 07:20:43: 18000000 INFO @ Sat, 03 Apr 2021 07:20:43: 28000000 INFO @ Sat, 03 Apr 2021 07:20:48: 21000000 INFO @ Sat, 03 Apr 2021 07:20:50: 19000000 INFO @ Sat, 03 Apr 2021 07:20:50: 29000000 INFO @ Sat, 03 Apr 2021 07:20:55: 22000000 INFO @ Sat, 03 Apr 2021 07:20:57: 20000000 INFO @ Sat, 03 Apr 2021 07:20:57: 30000000 INFO @ Sat, 03 Apr 2021 07:21:01: 23000000 INFO @ Sat, 03 Apr 2021 07:21:04: 21000000 INFO @ Sat, 03 Apr 2021 07:21:04: 31000000 INFO @ Sat, 03 Apr 2021 07:21:08: 24000000 INFO @ Sat, 03 Apr 2021 07:21:10: 22000000 INFO @ Sat, 03 Apr 2021 07:21:11: 32000000 INFO @ Sat, 03 Apr 2021 07:21:15: 25000000 INFO @ Sat, 03 Apr 2021 07:21:16: 23000000 INFO @ Sat, 03 Apr 2021 07:21:17: 33000000 INFO @ Sat, 03 Apr 2021 07:21:23: 26000000 INFO @ Sat, 03 Apr 2021 07:21:23: 24000000 INFO @ Sat, 03 Apr 2021 07:21:24: 34000000 INFO @ Sat, 03 Apr 2021 07:21:27: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:21:27: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:21:27: #1 total tags in treatment: 13132782 INFO @ Sat, 03 Apr 2021 07:21:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:21:27: #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 07:21:27: #1 tags after filtering in treatment: 10484756 INFO @ Sat, 03 Apr 2021 07:21:27: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 07:21:27: #1 finished! INFO @ Sat, 03 Apr 2021 07:21:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:21:28: #2 number of paired peaks: 240 WARNING @ Sat, 03 Apr 2021 07:21:28: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sat, 03 Apr 2021 07:21:28: start model_add_line... INFO @ Sat, 03 Apr 2021 07:21:28: start X-correlation... INFO @ Sat, 03 Apr 2021 07:21:28: end of X-cor INFO @ Sat, 03 Apr 2021 07:21:28: #2 finished! INFO @ Sat, 03 Apr 2021 07:21:28: #2 predicted fragment length is 69 bps INFO @ Sat, 03 Apr 2021 07:21:28: #2 alternative fragment length(s) may be 4,69,556 bps INFO @ Sat, 03 Apr 2021 07:21:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.05_model.r WARNING @ Sat, 03 Apr 2021 07:21:28: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:21:28: #2 You may need to consider one of the other alternative d(s): 4,69,556 WARNING @ Sat, 03 Apr 2021 07:21:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:21:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:21:29: 25000000 INFO @ Sat, 03 Apr 2021 07:21:30: 27000000 INFO @ Sat, 03 Apr 2021 07:21:35: 26000000 INFO @ Sat, 03 Apr 2021 07:21:38: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:21:42: 27000000 INFO @ Sat, 03 Apr 2021 07:21:45: 29000000 INFO @ Sat, 03 Apr 2021 07:21:48: 28000000 INFO @ Sat, 03 Apr 2021 07:21:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:21:52: 30000000 INFO @ Sat, 03 Apr 2021 07:21:53: 29000000 INFO @ Sat, 03 Apr 2021 07:21:59: 31000000 INFO @ Sat, 03 Apr 2021 07:21:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:21:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:21:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.05_summits.bed INFO @ Sat, 03 Apr 2021 07:21:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4889 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:21:59: 30000000 INFO @ Sat, 03 Apr 2021 07:22:05: 31000000 INFO @ Sat, 03 Apr 2021 07:22:05: 32000000 INFO @ Sat, 03 Apr 2021 07:22:11: 32000000 INFO @ Sat, 03 Apr 2021 07:22:12: 33000000 INFO @ Sat, 03 Apr 2021 07:22:17: 33000000 INFO @ Sat, 03 Apr 2021 07:22:19: 34000000 INFO @ Sat, 03 Apr 2021 07:22:21: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:22:21: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:22:21: #1 total tags in treatment: 13132782 INFO @ Sat, 03 Apr 2021 07:22:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:22:21: #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 07:22:21: #1 tags after filtering in treatment: 10484756 INFO @ Sat, 03 Apr 2021 07:22:21: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 07:22:21: #1 finished! INFO @ Sat, 03 Apr 2021 07:22:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:22:22: #2 number of paired peaks: 240 WARNING @ Sat, 03 Apr 2021 07:22:22: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sat, 03 Apr 2021 07:22:22: start model_add_line... INFO @ Sat, 03 Apr 2021 07:22:22: start X-correlation... INFO @ Sat, 03 Apr 2021 07:22:22: end of X-cor INFO @ Sat, 03 Apr 2021 07:22:22: #2 finished! INFO @ Sat, 03 Apr 2021 07:22:22: #2 predicted fragment length is 69 bps INFO @ Sat, 03 Apr 2021 07:22:22: #2 alternative fragment length(s) may be 4,69,556 bps INFO @ Sat, 03 Apr 2021 07:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.10_model.r WARNING @ Sat, 03 Apr 2021 07:22:22: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:22:22: #2 You may need to consider one of the other alternative d(s): 4,69,556 WARNING @ Sat, 03 Apr 2021 07:22:22: #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 07:22:22: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:22:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:22:23: 34000000 INFO @ Sat, 03 Apr 2021 07:22:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:22:25: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:22:25: #1 total tags in treatment: 13132782 INFO @ Sat, 03 Apr 2021 07:22:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:22:25: #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 07:22:25: #1 tags after filtering in treatment: 10484756 INFO @ Sat, 03 Apr 2021 07:22:25: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 07:22:25: #1 finished! INFO @ Sat, 03 Apr 2021 07:22:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:22:26: #2 number of paired peaks: 240 WARNING @ Sat, 03 Apr 2021 07:22:26: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sat, 03 Apr 2021 07:22:26: start model_add_line... INFO @ Sat, 03 Apr 2021 07:22:26: start X-correlation... INFO @ Sat, 03 Apr 2021 07:22:26: end of X-cor INFO @ Sat, 03 Apr 2021 07:22:26: #2 finished! INFO @ Sat, 03 Apr 2021 07:22:26: #2 predicted fragment length is 69 bps INFO @ Sat, 03 Apr 2021 07:22:26: #2 alternative fragment length(s) may be 4,69,556 bps INFO @ Sat, 03 Apr 2021 07:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.20_model.r WARNING @ Sat, 03 Apr 2021 07:22:26: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:22:26: #2 You may need to consider one of the other alternative d(s): 4,69,556 WARNING @ Sat, 03 Apr 2021 07:22:26: #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 07:22:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:22:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:22:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.10_summits.bed INFO @ Sat, 03 Apr 2021 07:22:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1885 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:22:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:22:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:22:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664620/SRX4664620.20_summits.bed INFO @ Sat, 03 Apr 2021 07:22:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 2 millis CompletedMACS2peakCalling