Job ID = 14168190 SRX = ERX3978836 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29080412 spots for ERR3975905/ERR3975905.sra Written 29080412 spots for ERR3975905/ERR3975905.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169409 ("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: 01:21:51 29080412 reads; of these: 29080412 (100.00%) were paired; of these: 3550373 (12.21%) aligned concordantly 0 times 19591532 (67.37%) aligned concordantly exactly 1 time 5938507 (20.42%) aligned concordantly >1 times ---- 3550373 pairs aligned concordantly 0 times; of these: 606462 (17.08%) aligned discordantly 1 time ---- 2943911 pairs aligned 0 times concordantly or discordantly; of these: 5887822 mates make up the pairs; of these: 3061138 (51.99%) aligned 0 times 1266248 (21.51%) aligned exactly 1 time 1560436 (26.50%) aligned >1 times 94.74% overall alignment rate Time searching: 01:21:52 Overall time: 01:21:52 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 24 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] 18226814 / 26017576 = 0.7006 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 17:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.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 17:35:04: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:35:04: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:35:09: 1000000 INFO @ Fri, 10 Dec 2021 17:35:15: 2000000 INFO @ Fri, 10 Dec 2021 17:35:21: 3000000 INFO @ Fri, 10 Dec 2021 17:35:26: 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 17:35:32: 5000000 INFO @ Fri, 10 Dec 2021 17:35:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.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 17:35:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:35:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:35:38: 6000000 INFO @ Fri, 10 Dec 2021 17:35:40: 1000000 INFO @ Fri, 10 Dec 2021 17:35:45: 7000000 INFO @ Fri, 10 Dec 2021 17:35:47: 2000000 INFO @ Fri, 10 Dec 2021 17:35:52: 8000000 INFO @ Fri, 10 Dec 2021 17:35:54: 3000000 INFO @ Fri, 10 Dec 2021 17:35:59: 9000000 INFO @ Fri, 10 Dec 2021 17:36:01: 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 17:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.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 17:36:04: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:36:04: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:36:06: 10000000 INFO @ Fri, 10 Dec 2021 17:36:08: 5000000 INFO @ Fri, 10 Dec 2021 17:36:12: 1000000 INFO @ Fri, 10 Dec 2021 17:36:13: 11000000 INFO @ Fri, 10 Dec 2021 17:36:16: 6000000 INFO @ Fri, 10 Dec 2021 17:36:20: 2000000 INFO @ Fri, 10 Dec 2021 17:36:20: 12000000 INFO @ Fri, 10 Dec 2021 17:36:23: 7000000 INFO @ Fri, 10 Dec 2021 17:36:27: 13000000 INFO @ Fri, 10 Dec 2021 17:36:27: 3000000 INFO @ Fri, 10 Dec 2021 17:36:30: 8000000 INFO @ Fri, 10 Dec 2021 17:36:35: 14000000 INFO @ Fri, 10 Dec 2021 17:36:35: 4000000 INFO @ Fri, 10 Dec 2021 17:36:37: 9000000 INFO @ Fri, 10 Dec 2021 17:36:42: 15000000 INFO @ Fri, 10 Dec 2021 17:36:43: 5000000 INFO @ Fri, 10 Dec 2021 17:36:44: 10000000 INFO @ Fri, 10 Dec 2021 17:36:49: 16000000 INFO @ Fri, 10 Dec 2021 17:36:51: 11000000 INFO @ Fri, 10 Dec 2021 17:36:51: 6000000 INFO @ Fri, 10 Dec 2021 17:36:56: 17000000 INFO @ Fri, 10 Dec 2021 17:36:58: 12000000 INFO @ Fri, 10 Dec 2021 17:36:59: 7000000 INFO @ Fri, 10 Dec 2021 17:37:03: 18000000 INFO @ Fri, 10 Dec 2021 17:37:06: 13000000 INFO @ Fri, 10 Dec 2021 17:37:07: 8000000 INFO @ Fri, 10 Dec 2021 17:37:08: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:37:08: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:37:08: #1 total tags in treatment: 7704287 INFO @ Fri, 10 Dec 2021 17:37:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:37:08: #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 17:37:08: #1 tags after filtering in treatment: 6956004 INFO @ Fri, 10 Dec 2021 17:37:08: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:37:08: #1 finished! INFO @ Fri, 10 Dec 2021 17:37:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:37:08: #2 number of paired peaks: 3370 INFO @ Fri, 10 Dec 2021 17:37:08: start model_add_line... INFO @ Fri, 10 Dec 2021 17:37:08: start X-correlation... INFO @ Fri, 10 Dec 2021 17:37:08: end of X-cor INFO @ Fri, 10 Dec 2021 17:37:08: #2 finished! INFO @ Fri, 10 Dec 2021 17:37:08: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Dec 2021 17:37:08: #2 alternative fragment length(s) may be 177 bps INFO @ Fri, 10 Dec 2021 17:37:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.05_model.r INFO @ Fri, 10 Dec 2021 17:37:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:37:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:37:13: 14000000 INFO @ Fri, 10 Dec 2021 17:37:15: 9000000 INFO @ Fri, 10 Dec 2021 17:37:20: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:37:23: 10000000 INFO @ Fri, 10 Dec 2021 17:37:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:37:27: 16000000 INFO @ Fri, 10 Dec 2021 17:37:31: 11000000 INFO @ Fri, 10 Dec 2021 17:37:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:37:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:37:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.05_summits.bed INFO @ Fri, 10 Dec 2021 17:37:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (10886 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:37:34: 17000000 INFO @ Fri, 10 Dec 2021 17:37:39: 12000000 INFO @ Fri, 10 Dec 2021 17:37:41: 18000000 INFO @ Fri, 10 Dec 2021 17:37:45: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:37:45: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:37:45: #1 total tags in treatment: 7704287 INFO @ Fri, 10 Dec 2021 17:37:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:37:45: #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 17:37:45: #1 tags after filtering in treatment: 6956004 INFO @ Fri, 10 Dec 2021 17:37:45: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:37:45: #1 finished! INFO @ Fri, 10 Dec 2021 17:37:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:37:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:37:46: #2 number of paired peaks: 3370 INFO @ Fri, 10 Dec 2021 17:37:46: start model_add_line... INFO @ Fri, 10 Dec 2021 17:37:46: start X-correlation... INFO @ Fri, 10 Dec 2021 17:37:46: end of X-cor INFO @ Fri, 10 Dec 2021 17:37:46: #2 finished! INFO @ Fri, 10 Dec 2021 17:37:46: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Dec 2021 17:37:46: #2 alternative fragment length(s) may be 177 bps INFO @ Fri, 10 Dec 2021 17:37:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.10_model.r INFO @ Fri, 10 Dec 2021 17:37:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:37:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:37:47: 13000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:37:55: 14000000 INFO @ Fri, 10 Dec 2021 17:38:02: 15000000 INFO @ Fri, 10 Dec 2021 17:38:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:38:09: 16000000 INFO @ Fri, 10 Dec 2021 17:38:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:38:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:38:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.10_summits.bed INFO @ Fri, 10 Dec 2021 17:38:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7609 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:38:16: 17000000 INFO @ Fri, 10 Dec 2021 17:38:23: 18000000 INFO @ Fri, 10 Dec 2021 17:38:28: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:38:28: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:38:28: #1 total tags in treatment: 7704287 INFO @ Fri, 10 Dec 2021 17:38:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:38:28: #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 17:38:28: #1 tags after filtering in treatment: 6956004 INFO @ Fri, 10 Dec 2021 17:38:28: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:38:28: #1 finished! INFO @ Fri, 10 Dec 2021 17:38:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:38:28: #2 number of paired peaks: 3370 INFO @ Fri, 10 Dec 2021 17:38:28: start model_add_line... INFO @ Fri, 10 Dec 2021 17:38:28: start X-correlation... INFO @ Fri, 10 Dec 2021 17:38:28: end of X-cor INFO @ Fri, 10 Dec 2021 17:38:28: #2 finished! INFO @ Fri, 10 Dec 2021 17:38:28: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Dec 2021 17:38:28: #2 alternative fragment length(s) may be 177 bps INFO @ Fri, 10 Dec 2021 17:38:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.20_model.r INFO @ Fri, 10 Dec 2021 17:38:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:38:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:38:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:38:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:38:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:38:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978836/ERX3978836.20_summits.bed INFO @ Fri, 10 Dec 2021 17:38:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4419 records, 4 fields): 6 millis CompletedMACS2peakCalling