Job ID = 14168721 SRX = ERX3978882 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 35975482 spots for ERR3975951/ERR3975951.sra Written 35975482 spots for ERR3975951/ERR3975951.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170033 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 02:44:56 35975482 reads; of these: 35975482 (100.00%) were paired; of these: 12207335 (33.93%) aligned concordantly 0 times 18826762 (52.33%) aligned concordantly exactly 1 time 4941385 (13.74%) aligned concordantly >1 times ---- 12207335 pairs aligned concordantly 0 times; of these: 1066091 (8.73%) aligned discordantly 1 time ---- 11141244 pairs aligned 0 times concordantly or discordantly; of these: 22282488 mates make up the pairs; of these: 11101585 (49.82%) aligned 0 times 7057257 (31.67%) aligned exactly 1 time 4123646 (18.51%) aligned >1 times 84.57% overall alignment rate Time searching: 02:44:57 Overall time: 02:44:57 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 28 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] 18462329 / 24419578 = 0.7560 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 23:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.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 23:01:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:01:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:01:24: 1000000 INFO @ Fri, 10 Dec 2021 23:01:32: 2000000 INFO @ Fri, 10 Dec 2021 23:01:40: 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 23:01:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.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 23:01:44: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:01:44: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:01:48: 4000000 INFO @ Fri, 10 Dec 2021 23:01:53: 1000000 INFO @ Fri, 10 Dec 2021 23:01:57: 5000000 INFO @ Fri, 10 Dec 2021 23:02:01: 2000000 INFO @ Fri, 10 Dec 2021 23:02:06: 6000000 INFO @ Fri, 10 Dec 2021 23:02:10: 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 23:02:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.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 23:02:14: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:02:14: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:02:16: 7000000 INFO @ Fri, 10 Dec 2021 23:02:20: 4000000 INFO @ Fri, 10 Dec 2021 23:02:24: 1000000 INFO @ Fri, 10 Dec 2021 23:02:26: 8000000 INFO @ Fri, 10 Dec 2021 23:02:29: 5000000 INFO @ Fri, 10 Dec 2021 23:02:33: 2000000 INFO @ Fri, 10 Dec 2021 23:02:35: 9000000 INFO @ Fri, 10 Dec 2021 23:02:39: 6000000 INFO @ Fri, 10 Dec 2021 23:02:43: 3000000 INFO @ Fri, 10 Dec 2021 23:02:45: 10000000 INFO @ Fri, 10 Dec 2021 23:02:50: 7000000 INFO @ Fri, 10 Dec 2021 23:02:52: 4000000 INFO @ Fri, 10 Dec 2021 23:02:54: 11000000 INFO @ Fri, 10 Dec 2021 23:03:00: 8000000 INFO @ Fri, 10 Dec 2021 23:03:03: 5000000 INFO @ Fri, 10 Dec 2021 23:03:03: 12000000 INFO @ Fri, 10 Dec 2021 23:03:10: 9000000 INFO @ Fri, 10 Dec 2021 23:03:13: 13000000 INFO @ Fri, 10 Dec 2021 23:03:14: 6000000 INFO @ Fri, 10 Dec 2021 23:03:19: 10000000 INFO @ Fri, 10 Dec 2021 23:03:24: 14000000 INFO @ Fri, 10 Dec 2021 23:03:25: 7000000 INFO @ Fri, 10 Dec 2021 23:03:29: 11000000 INFO @ Fri, 10 Dec 2021 23:03:33: 15000000 INFO @ Fri, 10 Dec 2021 23:03:36: 8000000 INFO @ Fri, 10 Dec 2021 23:03:39: 12000000 INFO @ Fri, 10 Dec 2021 23:03:43: 16000000 INFO @ Fri, 10 Dec 2021 23:03:47: 9000000 INFO @ Fri, 10 Dec 2021 23:03:49: 13000000 INFO @ Fri, 10 Dec 2021 23:03:53: 17000000 INFO @ Fri, 10 Dec 2021 23:03:58: 10000000 INFO @ Fri, 10 Dec 2021 23:04:00: 14000000 INFO @ Fri, 10 Dec 2021 23:04:04: 18000000 INFO @ Fri, 10 Dec 2021 23:04:08: 11000000 INFO @ Fri, 10 Dec 2021 23:04:12: 19000000 INFO @ Fri, 10 Dec 2021 23:04:12: 15000000 INFO @ Fri, 10 Dec 2021 23:04:17: 12000000 INFO @ Fri, 10 Dec 2021 23:04:21: 20000000 INFO @ Fri, 10 Dec 2021 23:04:26: 13000000 INFO @ Fri, 10 Dec 2021 23:04:27: 16000000 INFO @ Fri, 10 Dec 2021 23:04:29: 21000000 INFO @ Fri, 10 Dec 2021 23:04:36: 14000000 INFO @ Fri, 10 Dec 2021 23:04:38: 22000000 INFO @ Fri, 10 Dec 2021 23:04:41: 17000000 INFO @ Fri, 10 Dec 2021 23:04:46: 15000000 INFO @ Fri, 10 Dec 2021 23:04:46: 23000000 INFO @ Fri, 10 Dec 2021 23:04:53: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:04:53: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:04:53: #1 total tags in treatment: 5870310 INFO @ Fri, 10 Dec 2021 23:04:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:04:53: #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 23:04:53: #1 tags after filtering in treatment: 5345824 INFO @ Fri, 10 Dec 2021 23:04:53: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 23:04:53: #1 finished! INFO @ Fri, 10 Dec 2021 23:04:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:04:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:04:54: #2 number of paired peaks: 1702 INFO @ Fri, 10 Dec 2021 23:04:54: start model_add_line... INFO @ Fri, 10 Dec 2021 23:04:54: start X-correlation... INFO @ Fri, 10 Dec 2021 23:04:54: end of X-cor INFO @ Fri, 10 Dec 2021 23:04:54: #2 finished! INFO @ Fri, 10 Dec 2021 23:04:54: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 23:04:54: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 23:04:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.05_model.r WARNING @ Fri, 10 Dec 2021 23:04:54: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:04:54: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Fri, 10 Dec 2021 23:04:54: #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 23:04:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:04:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:04:54: 18000000 INFO @ Fri, 10 Dec 2021 23:04:55: 16000000 INFO @ Fri, 10 Dec 2021 23:05:05: 19000000 INFO @ Fri, 10 Dec 2021 23:05:05: 17000000 INFO @ Fri, 10 Dec 2021 23:05:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:05:13: 20000000 INFO @ Fri, 10 Dec 2021 23:05:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.05_peaks.xls INFO @ Fri, 10 Dec 2021 23:05:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:05:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.05_summits.bed INFO @ Fri, 10 Dec 2021 23:05:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6593 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:05:14: 18000000 INFO @ Fri, 10 Dec 2021 23:05:21: 21000000 INFO @ Fri, 10 Dec 2021 23:05:24: 19000000 INFO @ Fri, 10 Dec 2021 23:05:29: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 23:05:34: 20000000 INFO @ Fri, 10 Dec 2021 23:05:38: 23000000 INFO @ Fri, 10 Dec 2021 23:05:43: 21000000 INFO @ Fri, 10 Dec 2021 23:05:45: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:05:45: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:05:45: #1 total tags in treatment: 5870310 INFO @ Fri, 10 Dec 2021 23:05:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:05:45: #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 23:05:45: #1 tags after filtering in treatment: 5345824 INFO @ Fri, 10 Dec 2021 23:05:45: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 23:05:45: #1 finished! INFO @ Fri, 10 Dec 2021 23:05:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:05:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:05:46: #2 number of paired peaks: 1702 INFO @ Fri, 10 Dec 2021 23:05:46: start model_add_line... INFO @ Fri, 10 Dec 2021 23:05:46: start X-correlation... INFO @ Fri, 10 Dec 2021 23:05:46: end of X-cor INFO @ Fri, 10 Dec 2021 23:05:46: #2 finished! INFO @ Fri, 10 Dec 2021 23:05:46: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 23:05:46: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 23:05:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.10_model.r WARNING @ Fri, 10 Dec 2021 23:05:46: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:05:46: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Fri, 10 Dec 2021 23:05:46: #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 23:05:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:05:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:05:52: 22000000 INFO @ Fri, 10 Dec 2021 23:05:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:06:00: 23000000 INFO @ Fri, 10 Dec 2021 23:06:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.10_peaks.xls INFO @ Fri, 10 Dec 2021 23:06:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:06:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.10_summits.bed INFO @ Fri, 10 Dec 2021 23:06:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3091 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:06:07: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:06:07: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:06:07: #1 total tags in treatment: 5870310 INFO @ Fri, 10 Dec 2021 23:06:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:06:07: #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 23:06:07: #1 tags after filtering in treatment: 5345824 INFO @ Fri, 10 Dec 2021 23:06:07: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 23:06:07: #1 finished! INFO @ Fri, 10 Dec 2021 23:06:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:06:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:06:08: #2 number of paired peaks: 1702 INFO @ Fri, 10 Dec 2021 23:06:08: start model_add_line... INFO @ Fri, 10 Dec 2021 23:06:08: start X-correlation... INFO @ Fri, 10 Dec 2021 23:06:08: end of X-cor INFO @ Fri, 10 Dec 2021 23:06:08: #2 finished! INFO @ Fri, 10 Dec 2021 23:06:08: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 23:06:08: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 23:06:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.20_model.r WARNING @ Fri, 10 Dec 2021 23:06:08: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:06:08: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Fri, 10 Dec 2021 23:06:08: #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 23:06:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:06:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 23:06:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:06:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.20_peaks.xls INFO @ Fri, 10 Dec 2021 23:06:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:06:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978882/ERX3978882.20_summits.bed INFO @ Fri, 10 Dec 2021 23:06:28: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1096 records, 4 fields): 4 millis CompletedMACS2peakCalling