Job ID = 14168110 SRX = ERX3978942 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25371608 spots for ERR3976012/ERR3976012.sra Written 25371608 spots for ERR3976012/ERR3976012.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169441 ("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: 02:06:50 25371608 reads; of these: 25371608 (100.00%) were paired; of these: 8360001 (32.95%) aligned concordantly 0 times 12810860 (50.49%) aligned concordantly exactly 1 time 4200747 (16.56%) aligned concordantly >1 times ---- 8360001 pairs aligned concordantly 0 times; of these: 863104 (10.32%) aligned discordantly 1 time ---- 7496897 pairs aligned 0 times concordantly or discordantly; of these: 14993794 mates make up the pairs; of these: 6915802 (46.12%) aligned 0 times 4519049 (30.14%) aligned exactly 1 time 3558943 (23.74%) aligned >1 times 86.37% overall alignment rate Time searching: 02:06:51 Overall time: 02:06:51 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 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] 14091966 / 17534329 = 0.8037 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 17:48:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.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 17:48:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:48:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:48:17: 1000000 INFO @ Fri, 10 Dec 2021 17:48:22: 2000000 INFO @ Fri, 10 Dec 2021 17:48:28: 3000000 INFO @ Fri, 10 Dec 2021 17:48:33: 4000000 INFO @ Fri, 10 Dec 2021 17:48:39: 5000000 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 17:48:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.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 17:48:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:48:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:48:44: 6000000 INFO @ Fri, 10 Dec 2021 17:48:47: 1000000 INFO @ Fri, 10 Dec 2021 17:48:50: 7000000 INFO @ Fri, 10 Dec 2021 17:48:52: 2000000 INFO @ Fri, 10 Dec 2021 17:48:56: 8000000 INFO @ Fri, 10 Dec 2021 17:48:58: 3000000 INFO @ Fri, 10 Dec 2021 17:49:02: 9000000 INFO @ Fri, 10 Dec 2021 17:49:04: 4000000 INFO @ Fri, 10 Dec 2021 17:49:08: 10000000 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 17:49:10: 5000000 INFO @ Fri, 10 Dec 2021 17:49:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.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 17:49:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:49:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:49:15: 11000000 INFO @ Fri, 10 Dec 2021 17:49:17: 6000000 INFO @ Fri, 10 Dec 2021 17:49:18: 1000000 INFO @ Fri, 10 Dec 2021 17:49:21: 12000000 INFO @ Fri, 10 Dec 2021 17:49:23: 7000000 INFO @ Fri, 10 Dec 2021 17:49:25: 2000000 INFO @ Fri, 10 Dec 2021 17:49:28: 13000000 INFO @ Fri, 10 Dec 2021 17:49:29: 8000000 INFO @ Fri, 10 Dec 2021 17:49:32: 3000000 INFO @ Fri, 10 Dec 2021 17:49:35: 14000000 INFO @ Fri, 10 Dec 2021 17:49:36: 9000000 INFO @ Fri, 10 Dec 2021 17:49:40: 4000000 INFO @ Fri, 10 Dec 2021 17:49:41: 15000000 INFO @ Fri, 10 Dec 2021 17:49:42: 10000000 INFO @ Fri, 10 Dec 2021 17:49:45: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:49:45: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:49:45: #1 total tags in treatment: 3427255 INFO @ Fri, 10 Dec 2021 17:49:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:49:45: #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 17:49:45: #1 tags after filtering in treatment: 2900072 INFO @ Fri, 10 Dec 2021 17:49:45: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 17:49:45: #1 finished! INFO @ Fri, 10 Dec 2021 17:49:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:49:45: #2 number of paired peaks: 4184 INFO @ Fri, 10 Dec 2021 17:49:45: start model_add_line... INFO @ Fri, 10 Dec 2021 17:49:46: start X-correlation... INFO @ Fri, 10 Dec 2021 17:49:46: end of X-cor INFO @ Fri, 10 Dec 2021 17:49:46: #2 finished! INFO @ Fri, 10 Dec 2021 17:49:46: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Dec 2021 17:49:46: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Dec 2021 17:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.05_model.r WARNING @ Fri, 10 Dec 2021 17:49:46: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:49:46: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 10 Dec 2021 17:49:46: #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 17:49:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:49:47: 5000000 INFO @ Fri, 10 Dec 2021 17:49:49: 11000000 INFO @ Fri, 10 Dec 2021 17:49:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:49:54: 6000000 INFO @ Fri, 10 Dec 2021 17:49:55: 12000000 INFO @ Fri, 10 Dec 2021 17:49:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:49:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:49:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.05_summits.bed INFO @ Fri, 10 Dec 2021 17:49:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8328 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:50:01: 7000000 INFO @ Fri, 10 Dec 2021 17:50:02: 13000000 INFO @ Fri, 10 Dec 2021 17:50:08: 8000000 INFO @ Fri, 10 Dec 2021 17:50:09: 14000000 INFO @ Fri, 10 Dec 2021 17:50:15: 15000000 INFO @ Fri, 10 Dec 2021 17:50:16: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:50:19: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:50:19: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:50:19: #1 total tags in treatment: 3427255 INFO @ Fri, 10 Dec 2021 17:50:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:50:19: #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 17:50:19: #1 tags after filtering in treatment: 2900072 INFO @ Fri, 10 Dec 2021 17:50:19: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 17:50:19: #1 finished! INFO @ Fri, 10 Dec 2021 17:50:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:50:20: #2 number of paired peaks: 4184 INFO @ Fri, 10 Dec 2021 17:50:20: start model_add_line... INFO @ Fri, 10 Dec 2021 17:50:20: start X-correlation... INFO @ Fri, 10 Dec 2021 17:50:20: end of X-cor INFO @ Fri, 10 Dec 2021 17:50:20: #2 finished! INFO @ Fri, 10 Dec 2021 17:50:20: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Dec 2021 17:50:20: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Dec 2021 17:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.10_model.r WARNING @ Fri, 10 Dec 2021 17:50:20: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:50:20: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 10 Dec 2021 17:50:20: #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 17:50:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:50:23: 10000000 INFO @ Fri, 10 Dec 2021 17:50:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:50:30: 11000000 INFO @ Fri, 10 Dec 2021 17:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:50:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:50:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.10_summits.bed INFO @ Fri, 10 Dec 2021 17:50:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4097 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:50:37: 12000000 INFO @ Fri, 10 Dec 2021 17:50:45: 13000000 INFO @ Fri, 10 Dec 2021 17:50:52: 14000000 INFO @ Fri, 10 Dec 2021 17:50:59: 15000000 INFO @ Fri, 10 Dec 2021 17:51:03: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:51:03: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:51:03: #1 total tags in treatment: 3427255 INFO @ Fri, 10 Dec 2021 17:51:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:51:03: #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 17:51:03: #1 tags after filtering in treatment: 2900072 INFO @ Fri, 10 Dec 2021 17:51:03: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 17:51:03: #1 finished! INFO @ Fri, 10 Dec 2021 17:51:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:51:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:51:04: #2 number of paired peaks: 4184 INFO @ Fri, 10 Dec 2021 17:51:04: start model_add_line... INFO @ Fri, 10 Dec 2021 17:51:04: start X-correlation... INFO @ Fri, 10 Dec 2021 17:51:04: end of X-cor INFO @ Fri, 10 Dec 2021 17:51:04: #2 finished! INFO @ Fri, 10 Dec 2021 17:51:04: #2 predicted fragment length is 150 bps INFO @ Fri, 10 Dec 2021 17:51:04: #2 alternative fragment length(s) may be 150 bps INFO @ Fri, 10 Dec 2021 17:51:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.20_model.r WARNING @ Fri, 10 Dec 2021 17:51:04: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:51:04: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Fri, 10 Dec 2021 17:51:04: #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 17:51:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:51:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:51:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:51:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:51:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:51:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978942/ERX3978942.20_summits.bed INFO @ Fri, 10 Dec 2021 17:51:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1152 records, 4 fields): 3 millis CompletedMACS2peakCalling