Job ID = 14167377 SRX = ERX3978901 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 57106001 spots for ERR3975970/ERR3975970.sra Written 57106001 spots for ERR3975970/ERR3975970.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168806 ("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: 02:58:16 57106001 reads; of these: 57106001 (100.00%) were paired; of these: 8591001 (15.04%) aligned concordantly 0 times 37344930 (65.40%) aligned concordantly exactly 1 time 11170070 (19.56%) aligned concordantly >1 times ---- 8591001 pairs aligned concordantly 0 times; of these: 1451646 (16.90%) aligned discordantly 1 time ---- 7139355 pairs aligned 0 times concordantly or discordantly; of these: 14278710 mates make up the pairs; of these: 8697444 (60.91%) aligned 0 times 2736715 (19.17%) aligned exactly 1 time 2844551 (19.92%) aligned >1 times 92.38% overall alignment rate Time searching: 02:58:16 Overall time: 02:58:16 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] 34526542 / 49739771 = 0.6941 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 15:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.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 15:40:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:40:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:40:18: 1000000 INFO @ Fri, 10 Dec 2021 15:40:27: 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 15:40:34: 3000000 INFO @ Fri, 10 Dec 2021 15:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.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 15:40:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:40:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:40:44: 4000000 INFO @ Fri, 10 Dec 2021 15:40:45: 1000000 INFO @ Fri, 10 Dec 2021 15:40:53: 5000000 INFO @ Fri, 10 Dec 2021 15:40:54: 2000000 INFO @ Fri, 10 Dec 2021 15:41:01: 6000000 INFO @ Fri, 10 Dec 2021 15:41:02: 3000000 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 15:41:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.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 15:41:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:41:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:41:11: 7000000 INFO @ Fri, 10 Dec 2021 15:41:11: 4000000 INFO @ Fri, 10 Dec 2021 15:41:18: 1000000 INFO @ Fri, 10 Dec 2021 15:41:20: 8000000 INFO @ Fri, 10 Dec 2021 15:41:21: 5000000 INFO @ Fri, 10 Dec 2021 15:41:26: 2000000 INFO @ Fri, 10 Dec 2021 15:41:29: 9000000 INFO @ Fri, 10 Dec 2021 15:41:30: 6000000 INFO @ Fri, 10 Dec 2021 15:41:35: 3000000 INFO @ Fri, 10 Dec 2021 15:41:38: 7000000 INFO @ Fri, 10 Dec 2021 15:41:39: 10000000 INFO @ Fri, 10 Dec 2021 15:41:46: 4000000 INFO @ Fri, 10 Dec 2021 15:41:48: 8000000 INFO @ Fri, 10 Dec 2021 15:41:49: 11000000 INFO @ Fri, 10 Dec 2021 15:41:56: 5000000 INFO @ Fri, 10 Dec 2021 15:41:58: 12000000 INFO @ Fri, 10 Dec 2021 15:41:59: 9000000 INFO @ Fri, 10 Dec 2021 15:42:06: 6000000 INFO @ Fri, 10 Dec 2021 15:42:08: 13000000 INFO @ Fri, 10 Dec 2021 15:42:10: 10000000 INFO @ Fri, 10 Dec 2021 15:42:13: 7000000 INFO @ Fri, 10 Dec 2021 15:42:18: 14000000 INFO @ Fri, 10 Dec 2021 15:42:19: 11000000 INFO @ Fri, 10 Dec 2021 15:42:21: 8000000 INFO @ Fri, 10 Dec 2021 15:42:25: 15000000 INFO @ Fri, 10 Dec 2021 15:42:26: 12000000 INFO @ Fri, 10 Dec 2021 15:42:28: 9000000 INFO @ Fri, 10 Dec 2021 15:42:32: 16000000 INFO @ Fri, 10 Dec 2021 15:42:33: 13000000 INFO @ Fri, 10 Dec 2021 15:42:36: 10000000 INFO @ Fri, 10 Dec 2021 15:42:40: 17000000 INFO @ Fri, 10 Dec 2021 15:42:41: 14000000 INFO @ Fri, 10 Dec 2021 15:42:43: 11000000 INFO @ Fri, 10 Dec 2021 15:42:47: 18000000 INFO @ Fri, 10 Dec 2021 15:42:48: 15000000 INFO @ Fri, 10 Dec 2021 15:42:51: 12000000 INFO @ Fri, 10 Dec 2021 15:42:55: 19000000 INFO @ Fri, 10 Dec 2021 15:42:56: 16000000 INFO @ Fri, 10 Dec 2021 15:42:59: 13000000 INFO @ Fri, 10 Dec 2021 15:43:02: 20000000 INFO @ Fri, 10 Dec 2021 15:43:03: 17000000 INFO @ Fri, 10 Dec 2021 15:43:06: 14000000 INFO @ Fri, 10 Dec 2021 15:43:10: 21000000 INFO @ Fri, 10 Dec 2021 15:43:11: 18000000 INFO @ Fri, 10 Dec 2021 15:43:14: 15000000 INFO @ Fri, 10 Dec 2021 15:43:17: 22000000 INFO @ Fri, 10 Dec 2021 15:43:18: 19000000 INFO @ Fri, 10 Dec 2021 15:43:21: 16000000 INFO @ Fri, 10 Dec 2021 15:43:25: 23000000 INFO @ Fri, 10 Dec 2021 15:43:25: 20000000 INFO @ Fri, 10 Dec 2021 15:43:28: 17000000 INFO @ Fri, 10 Dec 2021 15:43:32: 24000000 INFO @ Fri, 10 Dec 2021 15:43:32: 21000000 INFO @ Fri, 10 Dec 2021 15:43:35: 18000000 INFO @ Fri, 10 Dec 2021 15:43:39: 25000000 INFO @ Fri, 10 Dec 2021 15:43:40: 22000000 INFO @ Fri, 10 Dec 2021 15:43:43: 19000000 INFO @ Fri, 10 Dec 2021 15:43:46: 26000000 INFO @ Fri, 10 Dec 2021 15:43:47: 23000000 INFO @ Fri, 10 Dec 2021 15:43:50: 20000000 INFO @ Fri, 10 Dec 2021 15:43:54: 27000000 INFO @ Fri, 10 Dec 2021 15:43:55: 24000000 INFO @ Fri, 10 Dec 2021 15:43:58: 21000000 INFO @ Fri, 10 Dec 2021 15:44:02: 28000000 INFO @ Fri, 10 Dec 2021 15:44:02: 25000000 INFO @ Fri, 10 Dec 2021 15:44:06: 22000000 INFO @ Fri, 10 Dec 2021 15:44:10: 29000000 INFO @ Fri, 10 Dec 2021 15:44:10: 26000000 INFO @ Fri, 10 Dec 2021 15:44:16: 23000000 INFO @ Fri, 10 Dec 2021 15:44:17: 30000000 INFO @ Fri, 10 Dec 2021 15:44:18: 27000000 INFO @ Fri, 10 Dec 2021 15:44:25: 24000000 INFO @ Fri, 10 Dec 2021 15:44:25: 31000000 INFO @ Fri, 10 Dec 2021 15:44:25: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:44:33: 32000000 INFO @ Fri, 10 Dec 2021 15:44:33: 29000000 INFO @ Fri, 10 Dec 2021 15:44:33: 25000000 INFO @ Fri, 10 Dec 2021 15:44:40: 33000000 INFO @ Fri, 10 Dec 2021 15:44:40: 30000000 INFO @ Fri, 10 Dec 2021 15:44:42: 26000000 INFO @ Fri, 10 Dec 2021 15:44:47: 34000000 INFO @ Fri, 10 Dec 2021 15:44:48: 31000000 INFO @ Fri, 10 Dec 2021 15:44:50: 27000000 INFO @ Fri, 10 Dec 2021 15:44:54: 35000000 INFO @ Fri, 10 Dec 2021 15:44:55: 32000000 INFO @ Fri, 10 Dec 2021 15:44:59: 28000000 INFO @ Fri, 10 Dec 2021 15:45:02: 36000000 INFO @ Fri, 10 Dec 2021 15:45:02: 33000000 INFO @ Fri, 10 Dec 2021 15:45:05: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:45:05: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:45:05: #1 total tags in treatment: 15021255 INFO @ Fri, 10 Dec 2021 15:45:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:45:05: #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 15:45:05: #1 tags after filtering in treatment: 13542249 INFO @ Fri, 10 Dec 2021 15:45:05: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 15:45:05: #1 finished! INFO @ Fri, 10 Dec 2021 15:45:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:45:07: #2 number of paired peaks: 840 WARNING @ Fri, 10 Dec 2021 15:45:07: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Fri, 10 Dec 2021 15:45:07: start model_add_line... INFO @ Fri, 10 Dec 2021 15:45:07: start X-correlation... INFO @ Fri, 10 Dec 2021 15:45:07: end of X-cor INFO @ Fri, 10 Dec 2021 15:45:07: #2 finished! INFO @ Fri, 10 Dec 2021 15:45:07: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 15:45:07: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 15:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.05_model.r INFO @ Fri, 10 Dec 2021 15:45:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:45:08: 29000000 INFO @ Fri, 10 Dec 2021 15:45:10: 34000000 INFO @ Fri, 10 Dec 2021 15:45:17: 35000000 INFO @ Fri, 10 Dec 2021 15:45:17: 30000000 INFO @ Fri, 10 Dec 2021 15:45:25: 36000000 INFO @ Fri, 10 Dec 2021 15:45:27: 31000000 INFO @ Fri, 10 Dec 2021 15:45:28: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:45:28: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:45:28: #1 total tags in treatment: 15021255 INFO @ Fri, 10 Dec 2021 15:45:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:45:28: #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 15:45:28: #1 tags after filtering in treatment: 13542249 INFO @ Fri, 10 Dec 2021 15:45:28: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 15:45:28: #1 finished! INFO @ Fri, 10 Dec 2021 15:45:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:45:30: #2 number of paired peaks: 840 WARNING @ Fri, 10 Dec 2021 15:45:30: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Fri, 10 Dec 2021 15:45:30: start model_add_line... INFO @ Fri, 10 Dec 2021 15:45:30: start X-correlation... INFO @ Fri, 10 Dec 2021 15:45:30: end of X-cor INFO @ Fri, 10 Dec 2021 15:45:30: #2 finished! INFO @ Fri, 10 Dec 2021 15:45:30: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 15:45:30: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 15:45:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.10_model.r INFO @ Fri, 10 Dec 2021 15:45:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:45:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:45:36: 32000000 INFO @ Fri, 10 Dec 2021 15:45:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:45:44: 33000000 INFO @ Fri, 10 Dec 2021 15:45:52: 34000000 INFO @ Fri, 10 Dec 2021 15:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.05_summits.bed INFO @ Fri, 10 Dec 2021 15:45:58: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12791 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:46:00: 35000000 INFO @ Fri, 10 Dec 2021 15:46:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:46:08: 36000000 INFO @ Fri, 10 Dec 2021 15:46:12: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 15:46:12: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 15:46:12: #1 total tags in treatment: 15021255 INFO @ Fri, 10 Dec 2021 15:46:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:46:12: #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 15:46:12: #1 tags after filtering in treatment: 13542249 INFO @ Fri, 10 Dec 2021 15:46:12: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 15:46:12: #1 finished! INFO @ Fri, 10 Dec 2021 15:46:12: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:46:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:46:13: #2 number of paired peaks: 840 WARNING @ Fri, 10 Dec 2021 15:46:13: Fewer paired peaks (840) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 840 pairs to build model! INFO @ Fri, 10 Dec 2021 15:46:13: start model_add_line... INFO @ Fri, 10 Dec 2021 15:46:13: start X-correlation... INFO @ Fri, 10 Dec 2021 15:46:13: end of X-cor INFO @ Fri, 10 Dec 2021 15:46:13: #2 finished! INFO @ Fri, 10 Dec 2021 15:46:13: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Dec 2021 15:46:13: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Dec 2021 15:46:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.20_model.r INFO @ Fri, 10 Dec 2021 15:46:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:46:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:46:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:46:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:46:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.10_summits.bed INFO @ Fri, 10 Dec 2021 15:46:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7206 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:46:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978901/ERX3978901.20_summits.bed INFO @ Fri, 10 Dec 2021 15:47:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2878 records, 4 fields): 5 millis CompletedMACS2peakCalling