Job ID = 14168045 SRX = ERX3978938 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30229114 spots for ERR3976008/ERR3976008.sra Written 30229114 spots for ERR3976008/ERR3976008.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169073 ("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: 01:44:13 30229114 reads; of these: 30229114 (100.00%) were paired; of these: 12579351 (41.61%) aligned concordantly 0 times 13638765 (45.12%) aligned concordantly exactly 1 time 4010998 (13.27%) aligned concordantly >1 times ---- 12579351 pairs aligned concordantly 0 times; of these: 1002007 (7.97%) aligned discordantly 1 time ---- 11577344 pairs aligned 0 times concordantly or discordantly; of these: 23154688 mates make up the pairs; of these: 11658295 (50.35%) aligned 0 times 7087619 (30.61%) aligned exactly 1 time 4408774 (19.04%) aligned >1 times 80.72% overall alignment rate Time searching: 01:44:14 Overall time: 01:44:14 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] 13534104 / 18290006 = 0.7400 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 16:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.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 16:40:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:40:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:40:57: 1000000 INFO @ Fri, 10 Dec 2021 16:41:04: 2000000 INFO @ Fri, 10 Dec 2021 16:41:11: 3000000 INFO @ Fri, 10 Dec 2021 16:41:18: 4000000 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 16:41:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.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 16:41:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:41:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:41:25: 5000000 INFO @ Fri, 10 Dec 2021 16:41:28: 1000000 INFO @ Fri, 10 Dec 2021 16:41:32: 6000000 INFO @ Fri, 10 Dec 2021 16:41:34: 2000000 INFO @ Fri, 10 Dec 2021 16:41:40: 7000000 INFO @ Fri, 10 Dec 2021 16:41:41: 3000000 INFO @ Fri, 10 Dec 2021 16:41:47: 8000000 INFO @ Fri, 10 Dec 2021 16:41:48: 4000000 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 16:41:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.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 16:41:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:41:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:41:55: 5000000 INFO @ Fri, 10 Dec 2021 16:41:55: 9000000 INFO @ Fri, 10 Dec 2021 16:41:58: 1000000 INFO @ Fri, 10 Dec 2021 16:42:02: 6000000 INFO @ Fri, 10 Dec 2021 16:42:02: 10000000 INFO @ Fri, 10 Dec 2021 16:42:06: 2000000 INFO @ Fri, 10 Dec 2021 16:42:08: 7000000 INFO @ Fri, 10 Dec 2021 16:42:10: 11000000 INFO @ Fri, 10 Dec 2021 16:42:14: 3000000 INFO @ Fri, 10 Dec 2021 16:42:15: 8000000 INFO @ Fri, 10 Dec 2021 16:42:17: 12000000 INFO @ Fri, 10 Dec 2021 16:42:22: 4000000 INFO @ Fri, 10 Dec 2021 16:42:22: 9000000 INFO @ Fri, 10 Dec 2021 16:42:25: 13000000 INFO @ Fri, 10 Dec 2021 16:42:29: 10000000 INFO @ Fri, 10 Dec 2021 16:42:30: 5000000 INFO @ Fri, 10 Dec 2021 16:42:33: 14000000 INFO @ Fri, 10 Dec 2021 16:42:36: 11000000 INFO @ Fri, 10 Dec 2021 16:42:38: 6000000 INFO @ Fri, 10 Dec 2021 16:42:40: 15000000 INFO @ Fri, 10 Dec 2021 16:42:43: 12000000 INFO @ Fri, 10 Dec 2021 16:42:45: 7000000 INFO @ Fri, 10 Dec 2021 16:42:48: 16000000 INFO @ Fri, 10 Dec 2021 16:42:50: 13000000 INFO @ Fri, 10 Dec 2021 16:42:53: 8000000 INFO @ Fri, 10 Dec 2021 16:42:56: 17000000 INFO @ Fri, 10 Dec 2021 16:42:57: 14000000 INFO @ Fri, 10 Dec 2021 16:43:01: 9000000 INFO @ Fri, 10 Dec 2021 16:43:04: 18000000 INFO @ Fri, 10 Dec 2021 16:43:04: 15000000 INFO @ Fri, 10 Dec 2021 16:43:08: 10000000 INFO @ Fri, 10 Dec 2021 16:43:12: 16000000 INFO @ Fri, 10 Dec 2021 16:43:12: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:43:16: 11000000 INFO @ Fri, 10 Dec 2021 16:43:19: 17000000 INFO @ Fri, 10 Dec 2021 16:43:20: 20000000 INFO @ Fri, 10 Dec 2021 16:43:24: 12000000 INFO @ Fri, 10 Dec 2021 16:43:26: 18000000 INFO @ Fri, 10 Dec 2021 16:43:27: 21000000 INFO @ Fri, 10 Dec 2021 16:43:31: 13000000 INFO @ Fri, 10 Dec 2021 16:43:33: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:43:33: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:43:33: #1 total tags in treatment: 4655578 INFO @ Fri, 10 Dec 2021 16:43:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:43:33: #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 16:43:33: #1 tags after filtering in treatment: 4247678 INFO @ Fri, 10 Dec 2021 16:43:33: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 16:43:33: #1 finished! INFO @ Fri, 10 Dec 2021 16:43:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:43:33: 19000000 INFO @ Fri, 10 Dec 2021 16:43:33: #2 number of paired peaks: 1244 INFO @ Fri, 10 Dec 2021 16:43:33: start model_add_line... INFO @ Fri, 10 Dec 2021 16:43:33: start X-correlation... INFO @ Fri, 10 Dec 2021 16:43:33: end of X-cor INFO @ Fri, 10 Dec 2021 16:43:33: #2 finished! INFO @ Fri, 10 Dec 2021 16:43:33: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 16:43:33: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 16:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.05_model.r WARNING @ Fri, 10 Dec 2021 16:43:33: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:43:33: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 16:43:33: #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 16:43:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:43:39: 14000000 INFO @ Fri, 10 Dec 2021 16:43:40: 20000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:43:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:43:47: 15000000 INFO @ Fri, 10 Dec 2021 16:43:47: 21000000 INFO @ Fri, 10 Dec 2021 16:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.05_summits.bed INFO @ Fri, 10 Dec 2021 16:43:47: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4449 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:43:52: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:43:52: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:43:52: #1 total tags in treatment: 4655578 INFO @ Fri, 10 Dec 2021 16:43:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:43:52: #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 16:43:52: #1 tags after filtering in treatment: 4247678 INFO @ Fri, 10 Dec 2021 16:43:52: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 16:43:52: #1 finished! INFO @ Fri, 10 Dec 2021 16:43:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:43:52: #2 number of paired peaks: 1244 INFO @ Fri, 10 Dec 2021 16:43:52: start model_add_line... INFO @ Fri, 10 Dec 2021 16:43:52: start X-correlation... INFO @ Fri, 10 Dec 2021 16:43:52: end of X-cor INFO @ Fri, 10 Dec 2021 16:43:52: #2 finished! INFO @ Fri, 10 Dec 2021 16:43:52: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 16:43:52: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 16:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.10_model.r WARNING @ Fri, 10 Dec 2021 16:43:52: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:43:52: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 16:43:52: #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 16:43:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:43:54: 16000000 INFO @ Fri, 10 Dec 2021 16:44:01: 17000000 INFO @ Fri, 10 Dec 2021 16:44:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.10_summits.bed INFO @ Fri, 10 Dec 2021 16:44:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1895 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:44:08: 18000000 INFO @ Fri, 10 Dec 2021 16:44:15: 19000000 INFO @ Fri, 10 Dec 2021 16:44:22: 20000000 INFO @ Fri, 10 Dec 2021 16:44:29: 21000000 INFO @ Fri, 10 Dec 2021 16:44:34: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:44:34: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:44:34: #1 total tags in treatment: 4655578 INFO @ Fri, 10 Dec 2021 16:44:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:44:34: #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 16:44:34: #1 tags after filtering in treatment: 4247678 INFO @ Fri, 10 Dec 2021 16:44:34: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 16:44:34: #1 finished! INFO @ Fri, 10 Dec 2021 16:44:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:44:35: #2 number of paired peaks: 1244 INFO @ Fri, 10 Dec 2021 16:44:35: start model_add_line... INFO @ Fri, 10 Dec 2021 16:44:35: start X-correlation... INFO @ Fri, 10 Dec 2021 16:44:35: end of X-cor INFO @ Fri, 10 Dec 2021 16:44:35: #2 finished! INFO @ Fri, 10 Dec 2021 16:44:35: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 16:44:35: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 16:44:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.20_model.r WARNING @ Fri, 10 Dec 2021 16:44:35: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:44:35: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 16:44:35: #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 16:44:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:44:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:44:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978938/ERX3978938.20_summits.bed INFO @ Fri, 10 Dec 2021 16:44:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (708 records, 4 fields): 2 millis CompletedMACS2peakCalling