Job ID = 14168095 SRX = ERX3978820 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22240808 spots for ERR3975867/ERR3975867.sra Written 22240808 spots for ERR3975867/ERR3975867.sra Read 25633296 spots for ERR3975883/ERR3975883.sra Written 25633296 spots for ERR3975883/ERR3975883.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169601 ("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: 03:08:51 47874104 reads; of these: 47874104 (100.00%) were paired; of these: 12301917 (25.70%) aligned concordantly 0 times 26003750 (54.32%) aligned concordantly exactly 1 time 9568437 (19.99%) aligned concordantly >1 times ---- 12301917 pairs aligned concordantly 0 times; of these: 3322332 (27.01%) aligned discordantly 1 time ---- 8979585 pairs aligned 0 times concordantly or discordantly; of these: 17959170 mates make up the pairs; of these: 15007451 (83.56%) aligned 0 times 871482 (4.85%) aligned exactly 1 time 2080237 (11.58%) aligned >1 times 84.33% overall alignment rate Time searching: 03:08:51 Overall time: 03:08:51 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 44 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] 29501170 / 38612111 = 0.7640 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 19:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.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 19:07:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:07:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:07:25: 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 19:07:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.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 19:07:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:07:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:07:44: 1000000 INFO @ Fri, 10 Dec 2021 19:07:48: 2000000 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 19:07:59: 2000000 INFO @ Fri, 10 Dec 2021 19:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.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 19:08:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:08:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:08:12: 3000000 INFO @ Fri, 10 Dec 2021 19:08:16: 3000000 INFO @ Fri, 10 Dec 2021 19:08:18: 1000000 INFO @ Fri, 10 Dec 2021 19:08:32: 4000000 INFO @ Fri, 10 Dec 2021 19:08:33: 2000000 INFO @ Fri, 10 Dec 2021 19:08:36: 4000000 INFO @ Fri, 10 Dec 2021 19:08:46: 5000000 INFO @ Fri, 10 Dec 2021 19:08:49: 3000000 INFO @ Fri, 10 Dec 2021 19:08:55: 5000000 INFO @ Fri, 10 Dec 2021 19:09:00: 6000000 INFO @ Fri, 10 Dec 2021 19:09:07: 4000000 INFO @ Fri, 10 Dec 2021 19:09:14: 7000000 INFO @ Fri, 10 Dec 2021 19:09:19: 6000000 INFO @ Fri, 10 Dec 2021 19:09:22: 5000000 INFO @ Fri, 10 Dec 2021 19:09:29: 8000000 INFO @ Fri, 10 Dec 2021 19:09:36: 6000000 INFO @ Fri, 10 Dec 2021 19:09:38: 7000000 INFO @ Fri, 10 Dec 2021 19:09:44: 9000000 INFO @ Fri, 10 Dec 2021 19:09:51: 7000000 INFO @ Fri, 10 Dec 2021 19:10:01: 10000000 INFO @ Fri, 10 Dec 2021 19:10:03: 8000000 INFO @ Fri, 10 Dec 2021 19:10:08: 8000000 INFO @ Fri, 10 Dec 2021 19:10:16: 11000000 INFO @ Fri, 10 Dec 2021 19:10:23: 9000000 INFO @ Fri, 10 Dec 2021 19:10:25: 9000000 INFO @ Fri, 10 Dec 2021 19:10:31: 12000000 INFO @ Fri, 10 Dec 2021 19:10:39: 10000000 INFO @ Fri, 10 Dec 2021 19:10:45: 13000000 INFO @ Fri, 10 Dec 2021 19:10:47: 10000000 INFO @ Fri, 10 Dec 2021 19:10:55: 11000000 INFO @ Fri, 10 Dec 2021 19:11:01: 14000000 INFO @ Fri, 10 Dec 2021 19:11:11: 11000000 INFO @ Fri, 10 Dec 2021 19:11:11: 12000000 INFO @ Fri, 10 Dec 2021 19:11:18: 15000000 INFO @ Fri, 10 Dec 2021 19:11:26: 13000000 INFO @ Fri, 10 Dec 2021 19:11:33: 12000000 INFO @ Fri, 10 Dec 2021 19:11:34: 16000000 INFO @ Fri, 10 Dec 2021 19:11:41: 14000000 INFO @ Fri, 10 Dec 2021 19:11:49: 17000000 INFO @ Fri, 10 Dec 2021 19:11:55: 13000000 INFO @ Fri, 10 Dec 2021 19:11:56: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:12:05: 18000000 INFO @ Fri, 10 Dec 2021 19:12:12: 16000000 INFO @ Fri, 10 Dec 2021 19:12:18: 14000000 INFO @ Fri, 10 Dec 2021 19:12:21: 19000000 INFO @ Fri, 10 Dec 2021 19:12:27: 17000000 INFO @ Fri, 10 Dec 2021 19:12:37: 20000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:12:43: 18000000 INFO @ Fri, 10 Dec 2021 19:12:45: 15000000 INFO @ Fri, 10 Dec 2021 19:12:53: 21000000 INFO @ Fri, 10 Dec 2021 19:12:59: 19000000 INFO @ Fri, 10 Dec 2021 19:13:05: #1 tag size is determined as 120 bps INFO @ Fri, 10 Dec 2021 19:13:05: #1 tag size = 120 INFO @ Fri, 10 Dec 2021 19:13:05: #1 total tags in treatment: 8282331 INFO @ Fri, 10 Dec 2021 19:13:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:13:05: #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 19:13:05: #1 tags after filtering in treatment: 6326977 INFO @ Fri, 10 Dec 2021 19:13:05: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 10 Dec 2021 19:13:05: #1 finished! INFO @ Fri, 10 Dec 2021 19:13:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:13:06: #2 number of paired peaks: 3194 INFO @ Fri, 10 Dec 2021 19:13:06: start model_add_line... INFO @ Fri, 10 Dec 2021 19:13:06: start X-correlation... INFO @ Fri, 10 Dec 2021 19:13:06: end of X-cor INFO @ Fri, 10 Dec 2021 19:13:06: #2 finished! INFO @ Fri, 10 Dec 2021 19:13:06: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 19:13:06: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 19:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.10_model.r WARNING @ Fri, 10 Dec 2021 19:13:06: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:13:06: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 19:13:06: #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 19:13:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:13:10: 16000000 INFO @ Fri, 10 Dec 2021 19:13:13: 20000000 INFO @ Fri, 10 Dec 2021 19:13:25: 21000000 INFO @ Fri, 10 Dec 2021 19:13:30: 17000000 INFO @ Fri, 10 Dec 2021 19:13:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:13:36: #1 tag size is determined as 120 bps INFO @ Fri, 10 Dec 2021 19:13:36: #1 tag size = 120 INFO @ Fri, 10 Dec 2021 19:13:36: #1 total tags in treatment: 8282331 INFO @ Fri, 10 Dec 2021 19:13:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:13:36: #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 19:13:36: #1 tags after filtering in treatment: 6326977 INFO @ Fri, 10 Dec 2021 19:13:36: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 10 Dec 2021 19:13:36: #1 finished! INFO @ Fri, 10 Dec 2021 19:13:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:13:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:13:37: #2 number of paired peaks: 3194 INFO @ Fri, 10 Dec 2021 19:13:37: start model_add_line... INFO @ Fri, 10 Dec 2021 19:13:37: start X-correlation... INFO @ Fri, 10 Dec 2021 19:13:38: end of X-cor INFO @ Fri, 10 Dec 2021 19:13:38: #2 finished! INFO @ Fri, 10 Dec 2021 19:13:38: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 19:13:38: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 19:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.20_model.r WARNING @ Fri, 10 Dec 2021 19:13:38: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:13:38: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 19:13:38: #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 19:13:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:13:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:13:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.10_summits.bed INFO @ Fri, 10 Dec 2021 19:13:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7768 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:13:51: 18000000 INFO @ Fri, 10 Dec 2021 19:14:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:14:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:14:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:14:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.20_summits.bed INFO @ Fri, 10 Dec 2021 19:14:16: Done! pass1 - making usageList (15 chroms): 9 millis pass2 - checking and writing primary data (3495 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:14:16: 19000000 INFO @ Fri, 10 Dec 2021 19:14:35: 20000000 INFO @ Fri, 10 Dec 2021 19:14:58: 21000000 INFO @ Fri, 10 Dec 2021 19:15:13: #1 tag size is determined as 120 bps INFO @ Fri, 10 Dec 2021 19:15:13: #1 tag size = 120 INFO @ Fri, 10 Dec 2021 19:15:13: #1 total tags in treatment: 8282331 INFO @ Fri, 10 Dec 2021 19:15:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:15:13: #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 19:15:13: #1 tags after filtering in treatment: 6326977 INFO @ Fri, 10 Dec 2021 19:15:13: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 10 Dec 2021 19:15:13: #1 finished! INFO @ Fri, 10 Dec 2021 19:15:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:15:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:15:14: #2 number of paired peaks: 3194 INFO @ Fri, 10 Dec 2021 19:15:14: start model_add_line... INFO @ Fri, 10 Dec 2021 19:15:14: start X-correlation... INFO @ Fri, 10 Dec 2021 19:15:14: end of X-cor INFO @ Fri, 10 Dec 2021 19:15:14: #2 finished! INFO @ Fri, 10 Dec 2021 19:15:14: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 19:15:14: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 19:15:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.05_model.r WARNING @ Fri, 10 Dec 2021 19:15:14: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:15:14: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 19:15:14: #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 19:15:14: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:15:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:15:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978820/ERX3978820.05_summits.bed INFO @ Fri, 10 Dec 2021 19:16:02: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12471 records, 4 fields): 21 millis CompletedMACS2peakCalling