Job ID = 14168382 SRX = ERX3978743 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17363839 spots for ERR3975753/ERR3975753.sra Written 17363839 spots for ERR3975753/ERR3975753.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169660 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:43:48 17363839 reads; of these: 17363839 (100.00%) were paired; of these: 6894500 (39.71%) aligned concordantly 0 times 7019054 (40.42%) aligned concordantly exactly 1 time 3450285 (19.87%) aligned concordantly >1 times ---- 6894500 pairs aligned concordantly 0 times; of these: 2400081 (34.81%) aligned discordantly 1 time ---- 4494419 pairs aligned 0 times concordantly or discordantly; of these: 8988838 mates make up the pairs; of these: 6124383 (68.13%) aligned 0 times 389488 (4.33%) aligned exactly 1 time 2474967 (27.53%) aligned >1 times 82.36% overall alignment rate Time searching: 00:43:49 Overall time: 00:43:49 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] 2696087 / 12789962 = 0.2108 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 19:17:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.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 19:17:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:17:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:18:06: 1000000 INFO @ Fri, 10 Dec 2021 19:18:18: 2000000 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 19:18:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.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 19:18:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:18:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:18:31: 3000000 INFO @ Fri, 10 Dec 2021 19:18:34: 1000000 INFO @ Fri, 10 Dec 2021 19:18:45: 4000000 INFO @ Fri, 10 Dec 2021 19:18:46: 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 19:18:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.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 19:18:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:18:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:18:58: 5000000 INFO @ Fri, 10 Dec 2021 19:18:59: 3000000 INFO @ Fri, 10 Dec 2021 19:19:06: 1000000 INFO @ Fri, 10 Dec 2021 19:19:11: 6000000 INFO @ Fri, 10 Dec 2021 19:19:13: 4000000 INFO @ Fri, 10 Dec 2021 19:19:18: 2000000 INFO @ Fri, 10 Dec 2021 19:19:24: 7000000 INFO @ Fri, 10 Dec 2021 19:19:25: 5000000 INFO @ Fri, 10 Dec 2021 19:19:31: 3000000 INFO @ Fri, 10 Dec 2021 19:19:37: 6000000 INFO @ Fri, 10 Dec 2021 19:19:37: 8000000 INFO @ Fri, 10 Dec 2021 19:19:44: 4000000 INFO @ Fri, 10 Dec 2021 19:19:49: 7000000 INFO @ Fri, 10 Dec 2021 19:19:52: 9000000 INFO @ Fri, 10 Dec 2021 19:19:56: 5000000 INFO @ Fri, 10 Dec 2021 19:20:00: 8000000 INFO @ Fri, 10 Dec 2021 19:20:05: 10000000 INFO @ Fri, 10 Dec 2021 19:20:08: 6000000 INFO @ Fri, 10 Dec 2021 19:20:12: 9000000 INFO @ Fri, 10 Dec 2021 19:20:19: 11000000 INFO @ Fri, 10 Dec 2021 19:20:20: 7000000 INFO @ Fri, 10 Dec 2021 19:20:24: 10000000 INFO @ Fri, 10 Dec 2021 19:20:32: 8000000 INFO @ Fri, 10 Dec 2021 19:20:33: 12000000 INFO @ Fri, 10 Dec 2021 19:20:36: 11000000 INFO @ Fri, 10 Dec 2021 19:20:44: 9000000 INFO @ Fri, 10 Dec 2021 19:20:47: 13000000 INFO @ Fri, 10 Dec 2021 19:20:48: 12000000 INFO @ Fri, 10 Dec 2021 19:20:56: 10000000 INFO @ Fri, 10 Dec 2021 19:20:59: 13000000 INFO @ Fri, 10 Dec 2021 19:21:01: 14000000 INFO @ Fri, 10 Dec 2021 19:21:07: 11000000 INFO @ Fri, 10 Dec 2021 19:21:11: 14000000 INFO @ Fri, 10 Dec 2021 19:21:14: 15000000 INFO @ Fri, 10 Dec 2021 19:21:20: 12000000 INFO @ Fri, 10 Dec 2021 19:21:23: 15000000 INFO @ Fri, 10 Dec 2021 19:21:27: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:21:32: 13000000 INFO @ Fri, 10 Dec 2021 19:21:35: 16000000 INFO @ Fri, 10 Dec 2021 19:21:39: 17000000 INFO @ Fri, 10 Dec 2021 19:21:44: 14000000 INFO @ Fri, 10 Dec 2021 19:21:46: 17000000 INFO @ Fri, 10 Dec 2021 19:21:52: 18000000 INFO @ Fri, 10 Dec 2021 19:21:55: 15000000 INFO @ Fri, 10 Dec 2021 19:21:57: 18000000 INFO @ Fri, 10 Dec 2021 19:22:04: 19000000 INFO @ Fri, 10 Dec 2021 19:22:07: 16000000 INFO @ Fri, 10 Dec 2021 19:22:08: 19000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:22:17: 17000000 INFO @ Fri, 10 Dec 2021 19:22:17: 20000000 INFO @ Fri, 10 Dec 2021 19:22:19: 20000000 INFO @ Fri, 10 Dec 2021 19:22:31: 18000000 INFO @ Fri, 10 Dec 2021 19:22:31: 21000000 INFO @ Fri, 10 Dec 2021 19:22:33: 21000000 INFO @ Fri, 10 Dec 2021 19:22:43: 19000000 INFO @ Fri, 10 Dec 2021 19:22:45: 22000000 INFO @ Fri, 10 Dec 2021 19:22:46: 22000000 INFO @ Fri, 10 Dec 2021 19:22:56: 20000000 INFO @ Fri, 10 Dec 2021 19:22:58: 23000000 INFO @ Fri, 10 Dec 2021 19:22:58: 23000000 INFO @ Fri, 10 Dec 2021 19:23:01: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:23:01: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:23:01: #1 total tags in treatment: 7921418 INFO @ Fri, 10 Dec 2021 19:23:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:23:01: #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 19:23:01: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:23:01: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:23:01: #1 total tags in treatment: 7921418 INFO @ Fri, 10 Dec 2021 19:23:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:23:01: #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 19:23:01: #1 tags after filtering in treatment: 5946073 INFO @ Fri, 10 Dec 2021 19:23:01: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 19:23:01: #1 finished! INFO @ Fri, 10 Dec 2021 19:23:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:23:01: #1 tags after filtering in treatment: 5946073 INFO @ Fri, 10 Dec 2021 19:23:01: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 19:23:01: #1 finished! INFO @ Fri, 10 Dec 2021 19:23:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:23:02: #2 number of paired peaks: 4268 INFO @ Fri, 10 Dec 2021 19:23:02: start model_add_line... INFO @ Fri, 10 Dec 2021 19:23:02: #2 number of paired peaks: 4268 INFO @ Fri, 10 Dec 2021 19:23:02: start model_add_line... INFO @ Fri, 10 Dec 2021 19:23:02: start X-correlation... INFO @ Fri, 10 Dec 2021 19:23:02: end of X-cor INFO @ Fri, 10 Dec 2021 19:23:02: #2 finished! INFO @ Fri, 10 Dec 2021 19:23:02: #2 predicted fragment length is 211 bps INFO @ Fri, 10 Dec 2021 19:23:02: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 10 Dec 2021 19:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.05_model.r WARNING @ Fri, 10 Dec 2021 19:23:02: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:23:02: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Fri, 10 Dec 2021 19:23:02: #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 19:23:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:23:02: start X-correlation... INFO @ Fri, 10 Dec 2021 19:23:02: end of X-cor INFO @ Fri, 10 Dec 2021 19:23:02: #2 finished! INFO @ Fri, 10 Dec 2021 19:23:02: #2 predicted fragment length is 211 bps INFO @ Fri, 10 Dec 2021 19:23:02: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 10 Dec 2021 19:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.10_model.r WARNING @ Fri, 10 Dec 2021 19:23:02: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:23:02: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Fri, 10 Dec 2021 19:23:02: #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 19:23:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:23:07: 21000000 INFO @ Fri, 10 Dec 2021 19:23:17: 22000000 INFO @ Fri, 10 Dec 2021 19:23:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:23:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:23:28: 23000000 INFO @ Fri, 10 Dec 2021 19:23:30: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:23:30: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:23:30: #1 total tags in treatment: 7921418 INFO @ Fri, 10 Dec 2021 19:23:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:23:30: #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 19:23:30: #1 tags after filtering in treatment: 5946073 INFO @ Fri, 10 Dec 2021 19:23:30: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 10 Dec 2021 19:23:30: #1 finished! INFO @ Fri, 10 Dec 2021 19:23:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:23:31: #2 number of paired peaks: 4268 INFO @ Fri, 10 Dec 2021 19:23:31: start model_add_line... INFO @ Fri, 10 Dec 2021 19:23:31: start X-correlation... INFO @ Fri, 10 Dec 2021 19:23:31: end of X-cor INFO @ Fri, 10 Dec 2021 19:23:31: #2 finished! INFO @ Fri, 10 Dec 2021 19:23:31: #2 predicted fragment length is 211 bps INFO @ Fri, 10 Dec 2021 19:23:31: #2 alternative fragment length(s) may be 211 bps INFO @ Fri, 10 Dec 2021 19:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.20_model.r WARNING @ Fri, 10 Dec 2021 19:23:31: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:23:31: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Fri, 10 Dec 2021 19:23:31: #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 19:23:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.10_summits.bed INFO @ Fri, 10 Dec 2021 19:23:32: Done! INFO @ Fri, 10 Dec 2021 19:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.05_summits.bed INFO @ Fri, 10 Dec 2021 19:23:32: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6385 records, 4 fields): 10 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (10879 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:23:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:24:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:24:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:24:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978743/ERX3978743.20_summits.bed INFO @ Fri, 10 Dec 2021 19:24:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2456 records, 4 fields): 9 millis CompletedMACS2peakCalling