Job ID = 14168790 SRX = ERX3978770 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20075474 spots for ERR3975788/ERR3975788.sra Written 20075474 spots for ERR3975788/ERR3975788.sra Read 36678035 spots for ERR3975805/ERR3975805.sra Written 36678035 spots for ERR3975805/ERR3975805.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170011 ("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: 01:51:25 56753509 reads; of these: 56753509 (100.00%) were paired; of these: 23031049 (40.58%) aligned concordantly 0 times 1897664 (3.34%) aligned concordantly exactly 1 time 31824796 (56.08%) aligned concordantly >1 times ---- 23031049 pairs aligned concordantly 0 times; of these: 803650 (3.49%) aligned discordantly 1 time ---- 22227399 pairs aligned 0 times concordantly or discordantly; of these: 44454798 mates make up the pairs; of these: 20142171 (45.31%) aligned 0 times 625904 (1.41%) aligned exactly 1 time 23686723 (53.28%) aligned >1 times 82.25% overall alignment rate Time searching: 01:51:25 Overall time: 01:51:25 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 68 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] 29565026 / 34103011 = 0.8669 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 22:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.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 22:45:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:45:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:45:49: 1000000 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 22:46:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.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 22:46:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:46:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:46:05: 2000000 INFO @ Fri, 10 Dec 2021 22:46:20: 1000000 INFO @ Fri, 10 Dec 2021 22:46:23: 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 22:46:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.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 22:46:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:46:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:46:38: 2000000 INFO @ Fri, 10 Dec 2021 22:46:41: 4000000 INFO @ Fri, 10 Dec 2021 22:46:48: 1000000 INFO @ Fri, 10 Dec 2021 22:46:57: 3000000 INFO @ Fri, 10 Dec 2021 22:47:02: 5000000 INFO @ Fri, 10 Dec 2021 22:47:04: 2000000 INFO @ Fri, 10 Dec 2021 22:47:18: 4000000 INFO @ Fri, 10 Dec 2021 22:47:19: 3000000 INFO @ Fri, 10 Dec 2021 22:47:22: 6000000 INFO @ Fri, 10 Dec 2021 22:47:33: 4000000 INFO @ Fri, 10 Dec 2021 22:47:38: 5000000 INFO @ Fri, 10 Dec 2021 22:47:42: 7000000 INFO @ Fri, 10 Dec 2021 22:47:47: 5000000 INFO @ Fri, 10 Dec 2021 22:47:59: 6000000 INFO @ Fri, 10 Dec 2021 22:48:00: 6000000 INFO @ Fri, 10 Dec 2021 22:48:00: 8000000 INFO @ Fri, 10 Dec 2021 22:48:13: 7000000 INFO @ Fri, 10 Dec 2021 22:48:19: 9000000 INFO @ Fri, 10 Dec 2021 22:48:19: 7000000 INFO @ Fri, 10 Dec 2021 22:48:25: 8000000 INFO @ Fri, 10 Dec 2021 22:48:37: 9000000 INFO @ Fri, 10 Dec 2021 22:48:37: 10000000 INFO @ Fri, 10 Dec 2021 22:48:37: 8000000 INFO @ Fri, 10 Dec 2021 22:48:49: 10000000 INFO @ Fri, 10 Dec 2021 22:48:56: 11000000 INFO @ Fri, 10 Dec 2021 22:48:56: 9000000 INFO @ Fri, 10 Dec 2021 22:49:02: 11000000 INFO @ Fri, 10 Dec 2021 22:49:13: 12000000 INFO @ Fri, 10 Dec 2021 22:49:14: 12000000 INFO @ Fri, 10 Dec 2021 22:49:15: 10000000 INFO @ Fri, 10 Dec 2021 22:49:27: 13000000 INFO @ Fri, 10 Dec 2021 22:49:30: 13000000 INFO @ Fri, 10 Dec 2021 22:49:33: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:49:40: 14000000 INFO @ Fri, 10 Dec 2021 22:49:48: 14000000 INFO @ Fri, 10 Dec 2021 22:49:51: 12000000 INFO @ Fri, 10 Dec 2021 22:49:52: 15000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:50:04: 16000000 INFO @ Fri, 10 Dec 2021 22:50:06: 15000000 INFO @ Fri, 10 Dec 2021 22:50:09: 13000000 INFO @ Fri, 10 Dec 2021 22:50:17: 17000000 INFO @ Fri, 10 Dec 2021 22:50:23: 16000000 INFO @ Fri, 10 Dec 2021 22:50:27: 14000000 INFO @ Fri, 10 Dec 2021 22:50:29: 18000000 INFO @ Fri, 10 Dec 2021 22:50:40: 17000000 INFO @ Fri, 10 Dec 2021 22:50:42: 19000000 INFO @ Fri, 10 Dec 2021 22:50:45: 15000000 INFO @ Fri, 10 Dec 2021 22:50:54: 20000000 INFO @ Fri, 10 Dec 2021 22:50:56: 18000000 INFO @ Fri, 10 Dec 2021 22:51:03: 16000000 INFO @ Fri, 10 Dec 2021 22:51:07: 21000000 INFO @ Fri, 10 Dec 2021 22:51:13: 19000000 INFO @ Fri, 10 Dec 2021 22:51:20: 22000000 INFO @ Fri, 10 Dec 2021 22:51:21: 17000000 INFO @ Fri, 10 Dec 2021 22:51:30: 20000000 INFO @ Fri, 10 Dec 2021 22:51:32: 23000000 INFO @ Fri, 10 Dec 2021 22:51:39: 18000000 INFO @ Fri, 10 Dec 2021 22:51:44: 24000000 INFO @ Fri, 10 Dec 2021 22:51:49: 21000000 INFO @ Fri, 10 Dec 2021 22:51:55: 25000000 INFO @ Fri, 10 Dec 2021 22:51:56: 19000000 INFO @ Fri, 10 Dec 2021 22:52:07: 26000000 INFO @ Fri, 10 Dec 2021 22:52:07: 22000000 INFO @ Fri, 10 Dec 2021 22:52:14: 20000000 INFO @ Fri, 10 Dec 2021 22:52:18: 27000000 INFO @ Fri, 10 Dec 2021 22:52:23: 23000000 INFO @ Fri, 10 Dec 2021 22:52:28: 28000000 INFO @ Fri, 10 Dec 2021 22:52:33: 21000000 INFO @ Fri, 10 Dec 2021 22:52:39: 29000000 INFO @ Fri, 10 Dec 2021 22:52:41: 24000000 INFO @ Fri, 10 Dec 2021 22:52:50: 30000000 INFO @ Fri, 10 Dec 2021 22:52:51: 22000000 INFO @ Fri, 10 Dec 2021 22:52:58: 25000000 INFO @ Fri, 10 Dec 2021 22:53:02: 31000000 INFO @ Fri, 10 Dec 2021 22:53:08: 23000000 INFO @ Fri, 10 Dec 2021 22:53:13: 32000000 INFO @ Fri, 10 Dec 2021 22:53:15: 26000000 INFO @ Fri, 10 Dec 2021 22:53:25: 33000000 INFO @ Fri, 10 Dec 2021 22:53:26: 24000000 INFO @ Fri, 10 Dec 2021 22:53:32: 27000000 INFO @ Fri, 10 Dec 2021 22:53:38: 34000000 INFO @ Fri, 10 Dec 2021 22:53:41: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 22:53:41: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 22:53:41: #1 total tags in treatment: 4372470 INFO @ Fri, 10 Dec 2021 22:53:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:53:41: #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 22:53:41: #1 tags after filtering in treatment: 2034074 INFO @ Fri, 10 Dec 2021 22:53:41: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 10 Dec 2021 22:53:41: #1 finished! INFO @ Fri, 10 Dec 2021 22:53:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:53:42: #2 number of paired peaks: 4541 INFO @ Fri, 10 Dec 2021 22:53:42: start model_add_line... INFO @ Fri, 10 Dec 2021 22:53:42: start X-correlation... INFO @ Fri, 10 Dec 2021 22:53:42: end of X-cor INFO @ Fri, 10 Dec 2021 22:53:42: #2 finished! INFO @ Fri, 10 Dec 2021 22:53:42: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 22:53:42: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 22:53:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.20_model.r WARNING @ Fri, 10 Dec 2021 22:53:42: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:53:42: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Fri, 10 Dec 2021 22:53:42: #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 22:53:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:53:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:53:44: 25000000 INFO @ Fri, 10 Dec 2021 22:53:49: 28000000 INFO @ Fri, 10 Dec 2021 22:53:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:53:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:53:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:53:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.20_summits.bed INFO @ Fri, 10 Dec 2021 22:53:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (549 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:54:00: 26000000 INFO @ Fri, 10 Dec 2021 22:54:06: 29000000 INFO @ Fri, 10 Dec 2021 22:54:17: 27000000 INFO @ Fri, 10 Dec 2021 22:54:22: 30000000 INFO @ Fri, 10 Dec 2021 22:54:33: 28000000 INFO @ Fri, 10 Dec 2021 22:54:39: 31000000 INFO @ Fri, 10 Dec 2021 22:54:48: 29000000 INFO @ Fri, 10 Dec 2021 22:54:55: 32000000 INFO @ Fri, 10 Dec 2021 22:55:04: 30000000 INFO @ Fri, 10 Dec 2021 22:55:13: 33000000 INFO @ Fri, 10 Dec 2021 22:55:21: 31000000 INFO @ Fri, 10 Dec 2021 22:55:32: 34000000 INFO @ Fri, 10 Dec 2021 22:55:36: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 22:55:36: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 22:55:36: #1 total tags in treatment: 4372470 INFO @ Fri, 10 Dec 2021 22:55:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:55:36: #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 22:55:36: #1 tags after filtering in treatment: 2034074 INFO @ Fri, 10 Dec 2021 22:55:36: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 10 Dec 2021 22:55:36: #1 finished! INFO @ Fri, 10 Dec 2021 22:55:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:55:37: #2 number of paired peaks: 4541 INFO @ Fri, 10 Dec 2021 22:55:37: start model_add_line... INFO @ Fri, 10 Dec 2021 22:55:37: start X-correlation... INFO @ Fri, 10 Dec 2021 22:55:37: 32000000 INFO @ Fri, 10 Dec 2021 22:55:37: end of X-cor INFO @ Fri, 10 Dec 2021 22:55:37: #2 finished! INFO @ Fri, 10 Dec 2021 22:55:37: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 22:55:37: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 22:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.05_model.r WARNING @ Fri, 10 Dec 2021 22:55:37: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:55:37: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Fri, 10 Dec 2021 22:55:37: #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 22:55:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:55:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.05_summits.bed INFO @ Fri, 10 Dec 2021 22:55:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4350 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:55:50: 33000000 INFO @ Fri, 10 Dec 2021 22:56:06: 34000000 INFO @ Fri, 10 Dec 2021 22:56:10: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 22:56:10: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 22:56:10: #1 total tags in treatment: 4372470 INFO @ Fri, 10 Dec 2021 22:56:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:56:10: #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 22:56:10: #1 tags after filtering in treatment: 2034074 INFO @ Fri, 10 Dec 2021 22:56:10: #1 Redundant rate of treatment: 0.53 INFO @ Fri, 10 Dec 2021 22:56:10: #1 finished! INFO @ Fri, 10 Dec 2021 22:56:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:56:10: #2 number of paired peaks: 4541 INFO @ Fri, 10 Dec 2021 22:56:10: start model_add_line... INFO @ Fri, 10 Dec 2021 22:56:10: start X-correlation... INFO @ Fri, 10 Dec 2021 22:56:10: end of X-cor INFO @ Fri, 10 Dec 2021 22:56:10: #2 finished! INFO @ Fri, 10 Dec 2021 22:56:10: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 22:56:10: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 22:56:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.10_model.r WARNING @ Fri, 10 Dec 2021 22:56:10: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:56:10: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Fri, 10 Dec 2021 22:56:10: #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 22:56:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:56:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:56:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:56:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:56:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:56:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978770/ERX3978770.10_summits.bed INFO @ Fri, 10 Dec 2021 22:56:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1923 records, 4 fields): 5 millis CompletedMACS2peakCalling