Job ID = 14167466 SRX = ERX3978915 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 46986746 spots for ERR3975984/ERR3975984.sra Written 46986746 spots for ERR3975984/ERR3975984.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169035 ("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: 03:46:24 46986746 reads; of these: 46986746 (100.00%) were paired; of these: 18217096 (38.77%) aligned concordantly 0 times 21995901 (46.81%) aligned concordantly exactly 1 time 6773749 (14.42%) aligned concordantly >1 times ---- 18217096 pairs aligned concordantly 0 times; of these: 1787769 (9.81%) aligned discordantly 1 time ---- 16429327 pairs aligned 0 times concordantly or discordantly; of these: 32858654 mates make up the pairs; of these: 16889496 (51.40%) aligned 0 times 9573795 (29.14%) aligned exactly 1 time 6395363 (19.46%) aligned >1 times 82.03% overall alignment rate Time searching: 03:46:24 Overall time: 03:46:24 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 32 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] 22693532 / 29993748 = 0.7566 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 16:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.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 16:43:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:43:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:43:36: 1000000 INFO @ Fri, 10 Dec 2021 16:43:45: 2000000 INFO @ Fri, 10 Dec 2021 16:43:54: 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 16:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.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 16:43:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:43:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:44:02: 4000000 INFO @ Fri, 10 Dec 2021 16:44:06: 1000000 INFO @ Fri, 10 Dec 2021 16:44:12: 5000000 INFO @ Fri, 10 Dec 2021 16:44:15: 2000000 INFO @ Fri, 10 Dec 2021 16:44:21: 6000000 INFO @ Fri, 10 Dec 2021 16:44:23: 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 16:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.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 16:44:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:44:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:44:30: 7000000 INFO @ Fri, 10 Dec 2021 16:44:32: 4000000 INFO @ Fri, 10 Dec 2021 16:44:40: 8000000 INFO @ Fri, 10 Dec 2021 16:44:40: 1000000 INFO @ Fri, 10 Dec 2021 16:44:41: 5000000 INFO @ Fri, 10 Dec 2021 16:44:50: 9000000 INFO @ Fri, 10 Dec 2021 16:44:50: 6000000 INFO @ Fri, 10 Dec 2021 16:44:52: 2000000 INFO @ Fri, 10 Dec 2021 16:44:59: 7000000 INFO @ Fri, 10 Dec 2021 16:44:59: 10000000 INFO @ Fri, 10 Dec 2021 16:45:03: 3000000 INFO @ Fri, 10 Dec 2021 16:45:08: 8000000 INFO @ Fri, 10 Dec 2021 16:45:09: 11000000 INFO @ Fri, 10 Dec 2021 16:45:15: 4000000 INFO @ Fri, 10 Dec 2021 16:45:17: 9000000 INFO @ Fri, 10 Dec 2021 16:45:19: 12000000 INFO @ Fri, 10 Dec 2021 16:45:25: 10000000 INFO @ Fri, 10 Dec 2021 16:45:27: 5000000 INFO @ Fri, 10 Dec 2021 16:45:28: 13000000 INFO @ Fri, 10 Dec 2021 16:45:34: 11000000 INFO @ Fri, 10 Dec 2021 16:45:37: 14000000 INFO @ Fri, 10 Dec 2021 16:45:38: 6000000 INFO @ Fri, 10 Dec 2021 16:45:41: 12000000 INFO @ Fri, 10 Dec 2021 16:45:47: 15000000 INFO @ Fri, 10 Dec 2021 16:45:49: 7000000 INFO @ Fri, 10 Dec 2021 16:45:49: 13000000 INFO @ Fri, 10 Dec 2021 16:45:56: 16000000 INFO @ Fri, 10 Dec 2021 16:45:58: 14000000 INFO @ Fri, 10 Dec 2021 16:46:01: 8000000 INFO @ Fri, 10 Dec 2021 16:46:05: 17000000 INFO @ Fri, 10 Dec 2021 16:46:06: 15000000 INFO @ Fri, 10 Dec 2021 16:46:12: 9000000 INFO @ Fri, 10 Dec 2021 16:46:14: 16000000 INFO @ Fri, 10 Dec 2021 16:46:14: 18000000 INFO @ Fri, 10 Dec 2021 16:46:22: 17000000 INFO @ Fri, 10 Dec 2021 16:46:23: 10000000 INFO @ Fri, 10 Dec 2021 16:46:24: 19000000 INFO @ Fri, 10 Dec 2021 16:46:30: 18000000 INFO @ Fri, 10 Dec 2021 16:46:33: 20000000 INFO @ Fri, 10 Dec 2021 16:46:35: 11000000 INFO @ Fri, 10 Dec 2021 16:46:38: 19000000 INFO @ Fri, 10 Dec 2021 16:46:42: 21000000 INFO @ Fri, 10 Dec 2021 16:46:46: 20000000 INFO @ Fri, 10 Dec 2021 16:46:46: 12000000 INFO @ Fri, 10 Dec 2021 16:46:51: 22000000 INFO @ Fri, 10 Dec 2021 16:46:53: 21000000 INFO @ Fri, 10 Dec 2021 16:46:57: 13000000 INFO @ Fri, 10 Dec 2021 16:47:00: 23000000 INFO @ Fri, 10 Dec 2021 16:47:01: 22000000 INFO @ Fri, 10 Dec 2021 16:47:08: 14000000 INFO @ Fri, 10 Dec 2021 16:47:09: 23000000 INFO @ Fri, 10 Dec 2021 16:47:09: 24000000 INFO @ Fri, 10 Dec 2021 16:47:16: 24000000 INFO @ Fri, 10 Dec 2021 16:47:18: 25000000 INFO @ Fri, 10 Dec 2021 16:47:19: 15000000 INFO @ Fri, 10 Dec 2021 16:47:24: 25000000 INFO @ Fri, 10 Dec 2021 16:47:28: 26000000 INFO @ Fri, 10 Dec 2021 16:47:30: 16000000 INFO @ Fri, 10 Dec 2021 16:47:32: 26000000 INFO @ Fri, 10 Dec 2021 16:47:37: 27000000 INFO @ Fri, 10 Dec 2021 16:47:40: 27000000 INFO @ Fri, 10 Dec 2021 16:47:41: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:47:46: 28000000 INFO @ Fri, 10 Dec 2021 16:47:48: 28000000 INFO @ Fri, 10 Dec 2021 16:47:52: 18000000 INFO @ Fri, 10 Dec 2021 16:47:55: 29000000 INFO @ Fri, 10 Dec 2021 16:47:56: 29000000 INFO @ Fri, 10 Dec 2021 16:48:03: 19000000 INFO @ Fri, 10 Dec 2021 16:48:03: 30000000 INFO @ Fri, 10 Dec 2021 16:48:04: 30000000 INFO @ Fri, 10 Dec 2021 16:48:11: 31000000 INFO @ Fri, 10 Dec 2021 16:48:12: 31000000 INFO @ Fri, 10 Dec 2021 16:48:14: 20000000 INFO @ Fri, 10 Dec 2021 16:48:16: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:48:16: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:48:16: #1 total tags in treatment: 7125528 INFO @ Fri, 10 Dec 2021 16:48:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:48:16: #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 16:48:16: #1 tags after filtering in treatment: 6417399 INFO @ Fri, 10 Dec 2021 16:48:16: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 16:48:16: #1 finished! INFO @ Fri, 10 Dec 2021 16:48:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:48:17: #2 number of paired peaks: 1299 INFO @ Fri, 10 Dec 2021 16:48:17: start model_add_line... INFO @ Fri, 10 Dec 2021 16:48:17: start X-correlation... INFO @ Fri, 10 Dec 2021 16:48:17: end of X-cor INFO @ Fri, 10 Dec 2021 16:48:17: #2 finished! INFO @ Fri, 10 Dec 2021 16:48:17: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 16:48:17: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 16:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.10_model.r WARNING @ Fri, 10 Dec 2021 16:48:17: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:48:17: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 16:48:17: #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 16:48:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:48:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:48:18: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:48:18: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:48:18: #1 total tags in treatment: 7125528 INFO @ Fri, 10 Dec 2021 16:48:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:48:18: #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 16:48:19: #1 tags after filtering in treatment: 6417399 INFO @ Fri, 10 Dec 2021 16:48:19: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 16:48:19: #1 finished! INFO @ Fri, 10 Dec 2021 16:48:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:48:19: #2 number of paired peaks: 1299 INFO @ Fri, 10 Dec 2021 16:48:19: start model_add_line... INFO @ Fri, 10 Dec 2021 16:48:19: start X-correlation... INFO @ Fri, 10 Dec 2021 16:48:19: end of X-cor INFO @ Fri, 10 Dec 2021 16:48:19: #2 finished! INFO @ Fri, 10 Dec 2021 16:48:19: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 16:48:19: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 16:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.05_model.r WARNING @ Fri, 10 Dec 2021 16:48:19: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:48:19: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 16:48:19: #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 16:48:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:48:24: 21000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:48:35: 22000000 INFO @ Fri, 10 Dec 2021 16:48:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:48:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:48:45: 23000000 INFO @ Fri, 10 Dec 2021 16:48:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:48:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:48:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.10_summits.bed INFO @ Fri, 10 Dec 2021 16:48:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3423 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:48:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:48:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:48:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.05_summits.bed INFO @ Fri, 10 Dec 2021 16:48:51: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7755 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:48:56: 24000000 INFO @ Fri, 10 Dec 2021 16:49:07: 25000000 INFO @ Fri, 10 Dec 2021 16:49:18: 26000000 INFO @ Fri, 10 Dec 2021 16:49:29: 27000000 INFO @ Fri, 10 Dec 2021 16:49:40: 28000000 INFO @ Fri, 10 Dec 2021 16:49:51: 29000000 INFO @ Fri, 10 Dec 2021 16:50:01: 30000000 INFO @ Fri, 10 Dec 2021 16:50:12: 31000000 INFO @ Fri, 10 Dec 2021 16:50:19: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:50:19: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:50:19: #1 total tags in treatment: 7125528 INFO @ Fri, 10 Dec 2021 16:50:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:50:19: #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 16:50:19: #1 tags after filtering in treatment: 6417399 INFO @ Fri, 10 Dec 2021 16:50:19: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 16:50:19: #1 finished! INFO @ Fri, 10 Dec 2021 16:50:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:50:20: #2 number of paired peaks: 1299 INFO @ Fri, 10 Dec 2021 16:50:20: start model_add_line... INFO @ Fri, 10 Dec 2021 16:50:20: start X-correlation... INFO @ Fri, 10 Dec 2021 16:50:20: end of X-cor INFO @ Fri, 10 Dec 2021 16:50:20: #2 finished! INFO @ Fri, 10 Dec 2021 16:50:20: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 16:50:20: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 16:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.20_model.r WARNING @ Fri, 10 Dec 2021 16:50:20: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:50:20: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 16:50:20: #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 16:50:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:50:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978915/ERX3978915.20_summits.bed INFO @ Fri, 10 Dec 2021 16:50:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1178 records, 4 fields): 7 millis CompletedMACS2peakCalling