Job ID = 14167421 SRX = ERX3978907 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 40404998 spots for ERR3975976/ERR3975976.sra Written 40404998 spots for ERR3975976/ERR3975976.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168526 ("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: 01:52:44 40404998 reads; of these: 40404998 (100.00%) were paired; of these: 5999725 (14.85%) aligned concordantly 0 times 27367497 (67.73%) aligned concordantly exactly 1 time 7037776 (17.42%) aligned concordantly >1 times ---- 5999725 pairs aligned concordantly 0 times; of these: 950101 (15.84%) aligned discordantly 1 time ---- 5049624 pairs aligned 0 times concordantly or discordantly; of these: 10099248 mates make up the pairs; of these: 6066747 (60.07%) aligned 0 times 2004430 (19.85%) aligned exactly 1 time 2028071 (20.08%) aligned >1 times 92.49% overall alignment rate Time searching: 01:52:44 Overall time: 01:52:44 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 32 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] 24659121 / 35190876 = 0.7007 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 14:33:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.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 14:33:12: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:33:12: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:33:19: 1000000 INFO @ Fri, 10 Dec 2021 14:33:25: 2000000 INFO @ Fri, 10 Dec 2021 14:33:32: 3000000 INFO @ Fri, 10 Dec 2021 14:33:39: 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 14:33:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.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 14:33:42: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:33:42: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:33:46: 5000000 INFO @ Fri, 10 Dec 2021 14:33:51: 1000000 INFO @ Fri, 10 Dec 2021 14:33:54: 6000000 INFO @ Fri, 10 Dec 2021 14:34:00: 2000000 INFO @ Fri, 10 Dec 2021 14:34:02: 7000000 INFO @ Fri, 10 Dec 2021 14:34:09: 3000000 INFO @ Fri, 10 Dec 2021 14:34:09: 8000000 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 14:34:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.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 14:34:12: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:34:12: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:34:18: 9000000 INFO @ Fri, 10 Dec 2021 14:34:18: 4000000 INFO @ Fri, 10 Dec 2021 14:34:21: 1000000 INFO @ Fri, 10 Dec 2021 14:34:26: 10000000 INFO @ Fri, 10 Dec 2021 14:34:27: 5000000 INFO @ Fri, 10 Dec 2021 14:34:30: 2000000 INFO @ Fri, 10 Dec 2021 14:34:34: 11000000 INFO @ Fri, 10 Dec 2021 14:34:36: 6000000 INFO @ Fri, 10 Dec 2021 14:34:39: 3000000 INFO @ Fri, 10 Dec 2021 14:34:43: 12000000 INFO @ Fri, 10 Dec 2021 14:34:45: 7000000 INFO @ Fri, 10 Dec 2021 14:34:48: 4000000 INFO @ Fri, 10 Dec 2021 14:34:51: 13000000 INFO @ Fri, 10 Dec 2021 14:34:54: 8000000 INFO @ Fri, 10 Dec 2021 14:34:57: 5000000 INFO @ Fri, 10 Dec 2021 14:34:59: 14000000 INFO @ Fri, 10 Dec 2021 14:35:03: 9000000 INFO @ Fri, 10 Dec 2021 14:35:07: 6000000 INFO @ Fri, 10 Dec 2021 14:35:08: 15000000 INFO @ Fri, 10 Dec 2021 14:35:13: 10000000 INFO @ Fri, 10 Dec 2021 14:35:16: 7000000 INFO @ Fri, 10 Dec 2021 14:35:17: 16000000 INFO @ Fri, 10 Dec 2021 14:35:22: 11000000 INFO @ Fri, 10 Dec 2021 14:35:25: 8000000 INFO @ Fri, 10 Dec 2021 14:35:25: 17000000 INFO @ Fri, 10 Dec 2021 14:35:31: 12000000 INFO @ Fri, 10 Dec 2021 14:35:34: 9000000 INFO @ Fri, 10 Dec 2021 14:35:34: 18000000 INFO @ Fri, 10 Dec 2021 14:35:40: 13000000 INFO @ Fri, 10 Dec 2021 14:35:43: 10000000 INFO @ Fri, 10 Dec 2021 14:35:43: 19000000 INFO @ Fri, 10 Dec 2021 14:35:49: 14000000 INFO @ Fri, 10 Dec 2021 14:35:51: 20000000 INFO @ Fri, 10 Dec 2021 14:35:52: 11000000 INFO @ Fri, 10 Dec 2021 14:35:58: 15000000 INFO @ Fri, 10 Dec 2021 14:36:00: 21000000 INFO @ Fri, 10 Dec 2021 14:36:01: 12000000 INFO @ Fri, 10 Dec 2021 14:36:07: 16000000 INFO @ Fri, 10 Dec 2021 14:36:08: 22000000 INFO @ Fri, 10 Dec 2021 14:36:10: 13000000 INFO @ Fri, 10 Dec 2021 14:36:16: 23000000 INFO @ Fri, 10 Dec 2021 14:36:17: 17000000 INFO @ Fri, 10 Dec 2021 14:36:19: 14000000 INFO @ Fri, 10 Dec 2021 14:36:24: 24000000 INFO @ Fri, 10 Dec 2021 14:36:26: 18000000 INFO @ Fri, 10 Dec 2021 14:36:28: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:36:33: 25000000 INFO @ Fri, 10 Dec 2021 14:36:35: 19000000 INFO @ Fri, 10 Dec 2021 14:36:36: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 14:36:36: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 14:36:36: #1 total tags in treatment: 10416492 INFO @ Fri, 10 Dec 2021 14:36:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:36:36: #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 14:36:36: #1 tags after filtering in treatment: 9556372 INFO @ Fri, 10 Dec 2021 14:36:36: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 14:36:36: #1 finished! INFO @ Fri, 10 Dec 2021 14:36:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:36:37: 16000000 INFO @ Fri, 10 Dec 2021 14:36:37: #2 number of paired peaks: 855 WARNING @ Fri, 10 Dec 2021 14:36:37: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Fri, 10 Dec 2021 14:36:37: start model_add_line... INFO @ Fri, 10 Dec 2021 14:36:37: start X-correlation... INFO @ Fri, 10 Dec 2021 14:36:37: end of X-cor INFO @ Fri, 10 Dec 2021 14:36:37: #2 finished! INFO @ Fri, 10 Dec 2021 14:36:37: #2 predicted fragment length is 170 bps INFO @ Fri, 10 Dec 2021 14:36:37: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 10 Dec 2021 14:36:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.05_model.r INFO @ Fri, 10 Dec 2021 14:36:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:36:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:36:44: 20000000 INFO @ Fri, 10 Dec 2021 14:36:46: 17000000 INFO @ Fri, 10 Dec 2021 14:36:54: 21000000 INFO @ Fri, 10 Dec 2021 14:36:55: 18000000 INFO @ Fri, 10 Dec 2021 14:37:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:37:03: 22000000 INFO @ Fri, 10 Dec 2021 14:37:04: 19000000 INFO @ Fri, 10 Dec 2021 14:37:12: 23000000 INFO @ Fri, 10 Dec 2021 14:37:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:37:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:37:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.05_summits.bed INFO @ Fri, 10 Dec 2021 14:37:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9164 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:37:13: 20000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:37:20: 24000000 INFO @ Fri, 10 Dec 2021 14:37:22: 21000000 INFO @ Fri, 10 Dec 2021 14:37:29: 25000000 INFO @ Fri, 10 Dec 2021 14:37:31: 22000000 INFO @ Fri, 10 Dec 2021 14:37:33: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 14:37:33: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 14:37:33: #1 total tags in treatment: 10416492 INFO @ Fri, 10 Dec 2021 14:37:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:37:33: #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 14:37:33: #1 tags after filtering in treatment: 9556372 INFO @ Fri, 10 Dec 2021 14:37:33: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 14:37:33: #1 finished! INFO @ Fri, 10 Dec 2021 14:37:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:37:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:37:34: #2 number of paired peaks: 855 WARNING @ Fri, 10 Dec 2021 14:37:34: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Fri, 10 Dec 2021 14:37:34: start model_add_line... INFO @ Fri, 10 Dec 2021 14:37:34: start X-correlation... INFO @ Fri, 10 Dec 2021 14:37:34: end of X-cor INFO @ Fri, 10 Dec 2021 14:37:34: #2 finished! INFO @ Fri, 10 Dec 2021 14:37:34: #2 predicted fragment length is 170 bps INFO @ Fri, 10 Dec 2021 14:37:34: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 10 Dec 2021 14:37:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.10_model.r INFO @ Fri, 10 Dec 2021 14:37:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:37:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:37:39: 23000000 INFO @ Fri, 10 Dec 2021 14:37:47: 24000000 INFO @ Fri, 10 Dec 2021 14:37:55: 25000000 INFO @ Fri, 10 Dec 2021 14:37:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:37:58: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 14:37:58: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 14:37:58: #1 total tags in treatment: 10416492 INFO @ Fri, 10 Dec 2021 14:37:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:37:58: #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 14:37:58: #1 tags after filtering in treatment: 9556372 INFO @ Fri, 10 Dec 2021 14:37:58: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 14:37:58: #1 finished! INFO @ Fri, 10 Dec 2021 14:37:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:37:59: #2 number of paired peaks: 855 WARNING @ Fri, 10 Dec 2021 14:37:59: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Fri, 10 Dec 2021 14:37:59: start model_add_line... INFO @ Fri, 10 Dec 2021 14:37:59: start X-correlation... INFO @ Fri, 10 Dec 2021 14:37:59: end of X-cor INFO @ Fri, 10 Dec 2021 14:37:59: #2 finished! INFO @ Fri, 10 Dec 2021 14:37:59: #2 predicted fragment length is 170 bps INFO @ Fri, 10 Dec 2021 14:37:59: #2 alternative fragment length(s) may be 170 bps INFO @ Fri, 10 Dec 2021 14:37:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.20_model.r INFO @ Fri, 10 Dec 2021 14:37:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:37:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:38:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:38:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:38:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.10_summits.bed INFO @ Fri, 10 Dec 2021 14:38:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4776 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:38:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:38:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:38:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:38:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978907/ERX3978907.20_summits.bed INFO @ Fri, 10 Dec 2021 14:38:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1873 records, 4 fields): 3 millis CompletedMACS2peakCalling