Job ID = 14171776 SRX = SRX10386237 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21623217 spots for SRR14009302/SRR14009302.sra Written 21623217 spots for SRR14009302/SRR14009302.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172395 ("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: 00:40:40 21623217 reads; of these: 21623217 (100.00%) were paired; of these: 1981545 (9.16%) aligned concordantly 0 times 13438023 (62.15%) aligned concordantly exactly 1 time 6203649 (28.69%) aligned concordantly >1 times ---- 1981545 pairs aligned concordantly 0 times; of these: 81628 (4.12%) aligned discordantly 1 time ---- 1899917 pairs aligned 0 times concordantly or discordantly; of these: 3799834 mates make up the pairs; of these: 3111068 (81.87%) aligned 0 times 430015 (11.32%) aligned exactly 1 time 258751 (6.81%) aligned >1 times 92.81% overall alignment rate Time searching: 00:40:40 Overall time: 00:40:40 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] 2422569 / 19698705 = 0.1230 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 @ Sat, 11 Dec 2021 13:38:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.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 @ Sat, 11 Dec 2021 13:38:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:38:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:38:36: 1000000 INFO @ Sat, 11 Dec 2021 13:38:42: 2000000 INFO @ Sat, 11 Dec 2021 13:38:48: 3000000 INFO @ Sat, 11 Dec 2021 13:38:53: 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 @ Sat, 11 Dec 2021 13:38:59: 5000000 INFO @ Sat, 11 Dec 2021 13:39:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.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 @ Sat, 11 Dec 2021 13:39:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:39:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:39:05: 6000000 INFO @ Sat, 11 Dec 2021 13:39:06: 1000000 INFO @ Sat, 11 Dec 2021 13:39:11: 7000000 INFO @ Sat, 11 Dec 2021 13:39:13: 2000000 INFO @ Sat, 11 Dec 2021 13:39:17: 8000000 INFO @ Sat, 11 Dec 2021 13:39:20: 3000000 INFO @ Sat, 11 Dec 2021 13:39:24: 9000000 INFO @ Sat, 11 Dec 2021 13:39:26: 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 @ Sat, 11 Dec 2021 13:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.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 @ Sat, 11 Dec 2021 13:39:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:39:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:39:31: 10000000 INFO @ Sat, 11 Dec 2021 13:39:32: 5000000 INFO @ Sat, 11 Dec 2021 13:39:37: 1000000 INFO @ Sat, 11 Dec 2021 13:39:38: 11000000 INFO @ Sat, 11 Dec 2021 13:39:39: 6000000 INFO @ Sat, 11 Dec 2021 13:39:43: 2000000 INFO @ Sat, 11 Dec 2021 13:39:45: 12000000 INFO @ Sat, 11 Dec 2021 13:39:45: 7000000 INFO @ Sat, 11 Dec 2021 13:39:50: 3000000 INFO @ Sat, 11 Dec 2021 13:39:52: 8000000 INFO @ Sat, 11 Dec 2021 13:39:52: 13000000 INFO @ Sat, 11 Dec 2021 13:39:57: 4000000 INFO @ Sat, 11 Dec 2021 13:39:59: 9000000 INFO @ Sat, 11 Dec 2021 13:39:59: 14000000 INFO @ Sat, 11 Dec 2021 13:40:03: 5000000 INFO @ Sat, 11 Dec 2021 13:40:06: 10000000 INFO @ Sat, 11 Dec 2021 13:40:06: 15000000 INFO @ Sat, 11 Dec 2021 13:40:10: 6000000 INFO @ Sat, 11 Dec 2021 13:40:13: 16000000 INFO @ Sat, 11 Dec 2021 13:40:13: 11000000 INFO @ Sat, 11 Dec 2021 13:40:17: 7000000 INFO @ Sat, 11 Dec 2021 13:40:19: 17000000 INFO @ Sat, 11 Dec 2021 13:40:20: 12000000 INFO @ Sat, 11 Dec 2021 13:40:24: 8000000 INFO @ Sat, 11 Dec 2021 13:40:26: 18000000 INFO @ Sat, 11 Dec 2021 13:40:28: 13000000 INFO @ Sat, 11 Dec 2021 13:40:30: 9000000 INFO @ Sat, 11 Dec 2021 13:40:33: 19000000 INFO @ Sat, 11 Dec 2021 13:40:35: 14000000 INFO @ Sat, 11 Dec 2021 13:40:36: 10000000 INFO @ Sat, 11 Dec 2021 13:40:40: 20000000 INFO @ Sat, 11 Dec 2021 13:40:42: 15000000 INFO @ Sat, 11 Dec 2021 13:40:42: 11000000 INFO @ Sat, 11 Dec 2021 13:40:47: 21000000 INFO @ Sat, 11 Dec 2021 13:40:48: 16000000 INFO @ Sat, 11 Dec 2021 13:40:49: 12000000 INFO @ Sat, 11 Dec 2021 13:40:54: 22000000 INFO @ Sat, 11 Dec 2021 13:40:55: 17000000 INFO @ Sat, 11 Dec 2021 13:40:55: 13000000 INFO @ Sat, 11 Dec 2021 13:41:01: 23000000 INFO @ Sat, 11 Dec 2021 13:41:01: 14000000 INFO @ Sat, 11 Dec 2021 13:41:02: 18000000 INFO @ Sat, 11 Dec 2021 13:41:07: 15000000 INFO @ Sat, 11 Dec 2021 13:41:08: 24000000 INFO @ Sat, 11 Dec 2021 13:41:09: 19000000 INFO @ Sat, 11 Dec 2021 13:41:14: 16000000 INFO @ Sat, 11 Dec 2021 13:41:14: 25000000 INFO @ Sat, 11 Dec 2021 13:41:16: 20000000 INFO @ Sat, 11 Dec 2021 13:41:21: 17000000 INFO @ Sat, 11 Dec 2021 13:41:21: 26000000 INFO @ Sat, 11 Dec 2021 13:41:23: 21000000 INFO @ Sat, 11 Dec 2021 13:41:27: 18000000 INFO @ Sat, 11 Dec 2021 13:41:28: 27000000 INFO @ Sat, 11 Dec 2021 13:41:30: 22000000 INFO @ Sat, 11 Dec 2021 13:41:33: 19000000 INFO @ Sat, 11 Dec 2021 13:41:35: 28000000 INFO @ Sat, 11 Dec 2021 13:41:38: 23000000 INFO @ Sat, 11 Dec 2021 13:41:39: 20000000 INFO @ Sat, 11 Dec 2021 13:41:42: 29000000 INFO @ Sat, 11 Dec 2021 13:41:45: 24000000 INFO @ Sat, 11 Dec 2021 13:41:45: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:41:49: 30000000 INFO @ Sat, 11 Dec 2021 13:41:51: 25000000 INFO @ Sat, 11 Dec 2021 13:41:52: 22000000 INFO @ Sat, 11 Dec 2021 13:41:55: 31000000 INFO @ Sat, 11 Dec 2021 13:41:58: 23000000 INFO @ Sat, 11 Dec 2021 13:41:58: 26000000 INFO @ Sat, 11 Dec 2021 13:42:02: 32000000 INFO @ Sat, 11 Dec 2021 13:42:04: 24000000 INFO @ Sat, 11 Dec 2021 13:42:05: 27000000 INFO @ Sat, 11 Dec 2021 13:42:09: 33000000 INFO @ Sat, 11 Dec 2021 13:42:10: 25000000 INFO @ Sat, 11 Dec 2021 13:42:12: 28000000 INFO @ Sat, 11 Dec 2021 13:42:16: 34000000 INFO @ Sat, 11 Dec 2021 13:42:17: 26000000 INFO @ Sat, 11 Dec 2021 13:42:19: 29000000 INFO @ Sat, 11 Dec 2021 13:42:23: 27000000 INFO @ Sat, 11 Dec 2021 13:42:23: 35000000 INFO @ Sat, 11 Dec 2021 13:42:25: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:42:25: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:42:25: #1 total tags in treatment: 17220688 INFO @ Sat, 11 Dec 2021 13:42:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:42:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:42:26: #1 tags after filtering in treatment: 14505626 INFO @ Sat, 11 Dec 2021 13:42:26: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 13:42:26: #1 finished! INFO @ Sat, 11 Dec 2021 13:42:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:42:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:42:26: 30000000 INFO @ Sat, 11 Dec 2021 13:42:26: #2 number of paired peaks: 101 WARNING @ Sat, 11 Dec 2021 13:42:26: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 11 Dec 2021 13:42:26: start model_add_line... INFO @ Sat, 11 Dec 2021 13:42:27: start X-correlation... INFO @ Sat, 11 Dec 2021 13:42:27: end of X-cor INFO @ Sat, 11 Dec 2021 13:42:27: #2 finished! INFO @ Sat, 11 Dec 2021 13:42:27: #2 predicted fragment length is 105 bps INFO @ Sat, 11 Dec 2021 13:42:27: #2 alternative fragment length(s) may be 105,128 bps INFO @ Sat, 11 Dec 2021 13:42:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.05_model.r INFO @ Sat, 11 Dec 2021 13:42:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:42:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:42:29: 28000000 INFO @ Sat, 11 Dec 2021 13:42:33: 31000000 INFO @ Sat, 11 Dec 2021 13:42:35: 29000000 INFO @ Sat, 11 Dec 2021 13:42:40: 32000000 INFO @ Sat, 11 Dec 2021 13:42:41: 30000000 INFO @ Sat, 11 Dec 2021 13:42:47: 33000000 INFO @ Sat, 11 Dec 2021 13:42:48: 31000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:42:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:42:54: 32000000 INFO @ Sat, 11 Dec 2021 13:42:54: 34000000 INFO @ Sat, 11 Dec 2021 13:43:00: 33000000 INFO @ Sat, 11 Dec 2021 13:43:01: 35000000 INFO @ Sat, 11 Dec 2021 13:43:03: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:43:03: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:43:03: #1 total tags in treatment: 17220688 INFO @ Sat, 11 Dec 2021 13:43:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:43:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:43:04: #1 tags after filtering in treatment: 14505626 INFO @ Sat, 11 Dec 2021 13:43:04: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 13:43:04: #1 finished! INFO @ Sat, 11 Dec 2021 13:43:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:43:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:43:05: #2 number of paired peaks: 101 WARNING @ Sat, 11 Dec 2021 13:43:05: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 11 Dec 2021 13:43:05: start model_add_line... INFO @ Sat, 11 Dec 2021 13:43:05: start X-correlation... INFO @ Sat, 11 Dec 2021 13:43:05: end of X-cor INFO @ Sat, 11 Dec 2021 13:43:05: #2 finished! INFO @ Sat, 11 Dec 2021 13:43:05: #2 predicted fragment length is 105 bps INFO @ Sat, 11 Dec 2021 13:43:05: #2 alternative fragment length(s) may be 105,128 bps INFO @ Sat, 11 Dec 2021 13:43:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.10_model.r INFO @ Sat, 11 Dec 2021 13:43:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:43:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:43:06: 34000000 INFO @ Sat, 11 Dec 2021 13:43:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:43:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:43:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.05_summits.bed INFO @ Sat, 11 Dec 2021 13:43:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1244 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:43:11: 35000000 INFO @ Sat, 11 Dec 2021 13:43:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:43:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:43:13: #1 total tags in treatment: 17220688 INFO @ Sat, 11 Dec 2021 13:43:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:43:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:43:13: #1 tags after filtering in treatment: 14505626 INFO @ Sat, 11 Dec 2021 13:43:13: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 13:43:13: #1 finished! INFO @ Sat, 11 Dec 2021 13:43:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:43:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:43:14: #2 number of paired peaks: 101 WARNING @ Sat, 11 Dec 2021 13:43:14: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sat, 11 Dec 2021 13:43:14: start model_add_line... INFO @ Sat, 11 Dec 2021 13:43:14: start X-correlation... INFO @ Sat, 11 Dec 2021 13:43:14: end of X-cor INFO @ Sat, 11 Dec 2021 13:43:14: #2 finished! INFO @ Sat, 11 Dec 2021 13:43:14: #2 predicted fragment length is 105 bps INFO @ Sat, 11 Dec 2021 13:43:14: #2 alternative fragment length(s) may be 105,128 bps INFO @ Sat, 11 Dec 2021 13:43:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.20_model.r INFO @ Sat, 11 Dec 2021 13:43:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:43:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:43:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:43:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:43:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.10_summits.bed INFO @ Sat, 11 Dec 2021 13:43:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (846 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386237/SRX10386237.20_summits.bed INFO @ Sat, 11 Dec 2021 13:43:54: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (527 records, 4 fields): 2 millis CompletedMACS2peakCalling