Job ID = 14171694 SRX = SRX10386218 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22552421 spots for SRR14009283/SRR14009283.sra Written 22552421 spots for SRR14009283/SRR14009283.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172438 ("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: 01:07:08 22552421 reads; of these: 22552421 (100.00%) were paired; of these: 2920107 (12.95%) aligned concordantly 0 times 12378995 (54.89%) aligned concordantly exactly 1 time 7253319 (32.16%) aligned concordantly >1 times ---- 2920107 pairs aligned concordantly 0 times; of these: 478520 (16.39%) aligned discordantly 1 time ---- 2441587 pairs aligned 0 times concordantly or discordantly; of these: 4883174 mates make up the pairs; of these: 3831222 (78.46%) aligned 0 times 486238 (9.96%) aligned exactly 1 time 565714 (11.58%) aligned >1 times 91.51% overall alignment rate Time searching: 01:07:08 Overall time: 01:07:08 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] 2860944 / 20062044 = 0.1426 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 13:51:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.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 13:51:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:51:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:51:23: 1000000 INFO @ Sat, 11 Dec 2021 13:51:30: 2000000 INFO @ Sat, 11 Dec 2021 13:51:37: 3000000 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 13:51:44: 4000000 INFO @ Sat, 11 Dec 2021 13:51:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.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 13:51:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:51:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:51:52: 5000000 INFO @ Sat, 11 Dec 2021 13:51:54: 1000000 INFO @ Sat, 11 Dec 2021 13:51:59: 6000000 INFO @ Sat, 11 Dec 2021 13:52:02: 2000000 INFO @ Sat, 11 Dec 2021 13:52:06: 7000000 INFO @ Sat, 11 Dec 2021 13:52:11: 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 @ Sat, 11 Dec 2021 13:52:13: 8000000 INFO @ Sat, 11 Dec 2021 13:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.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 13:52:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:52:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:52:20: 4000000 INFO @ Sat, 11 Dec 2021 13:52:21: 9000000 INFO @ Sat, 11 Dec 2021 13:52:26: 1000000 INFO @ Sat, 11 Dec 2021 13:52:28: 10000000 INFO @ Sat, 11 Dec 2021 13:52:30: 5000000 INFO @ Sat, 11 Dec 2021 13:52:35: 11000000 INFO @ Sat, 11 Dec 2021 13:52:35: 2000000 INFO @ Sat, 11 Dec 2021 13:52:39: 6000000 INFO @ Sat, 11 Dec 2021 13:52:42: 12000000 INFO @ Sat, 11 Dec 2021 13:52:45: 3000000 INFO @ Sat, 11 Dec 2021 13:52:49: 13000000 INFO @ Sat, 11 Dec 2021 13:52:49: 7000000 INFO @ Sat, 11 Dec 2021 13:52:54: 4000000 INFO @ Sat, 11 Dec 2021 13:52:56: 14000000 INFO @ Sat, 11 Dec 2021 13:52:59: 8000000 INFO @ Sat, 11 Dec 2021 13:53:03: 15000000 INFO @ Sat, 11 Dec 2021 13:53:04: 5000000 INFO @ Sat, 11 Dec 2021 13:53:09: 9000000 INFO @ Sat, 11 Dec 2021 13:53:10: 16000000 INFO @ Sat, 11 Dec 2021 13:53:14: 6000000 INFO @ Sat, 11 Dec 2021 13:53:17: 17000000 INFO @ Sat, 11 Dec 2021 13:53:19: 10000000 INFO @ Sat, 11 Dec 2021 13:53:24: 18000000 INFO @ Sat, 11 Dec 2021 13:53:24: 7000000 INFO @ Sat, 11 Dec 2021 13:53:29: 11000000 INFO @ Sat, 11 Dec 2021 13:53:31: 19000000 INFO @ Sat, 11 Dec 2021 13:53:34: 8000000 INFO @ Sat, 11 Dec 2021 13:53:38: 12000000 INFO @ Sat, 11 Dec 2021 13:53:38: 20000000 INFO @ Sat, 11 Dec 2021 13:53:43: 9000000 INFO @ Sat, 11 Dec 2021 13:53:45: 21000000 INFO @ Sat, 11 Dec 2021 13:53:47: 13000000 INFO @ Sat, 11 Dec 2021 13:53:53: 22000000 INFO @ Sat, 11 Dec 2021 13:53:53: 10000000 INFO @ Sat, 11 Dec 2021 13:53:56: 14000000 INFO @ Sat, 11 Dec 2021 13:54:00: 23000000 INFO @ Sat, 11 Dec 2021 13:54:03: 11000000 INFO @ Sat, 11 Dec 2021 13:54:06: 15000000 INFO @ Sat, 11 Dec 2021 13:54:07: 24000000 INFO @ Sat, 11 Dec 2021 13:54:12: 12000000 INFO @ Sat, 11 Dec 2021 13:54:14: 25000000 INFO @ Sat, 11 Dec 2021 13:54:15: 16000000 INFO @ Sat, 11 Dec 2021 13:54:21: 26000000 INFO @ Sat, 11 Dec 2021 13:54:22: 13000000 INFO @ Sat, 11 Dec 2021 13:54:24: 17000000 INFO @ Sat, 11 Dec 2021 13:54:28: 27000000 INFO @ Sat, 11 Dec 2021 13:54:32: 14000000 INFO @ Sat, 11 Dec 2021 13:54:33: 18000000 INFO @ Sat, 11 Dec 2021 13:54:35: 28000000 INFO @ Sat, 11 Dec 2021 13:54:41: 15000000 INFO @ Sat, 11 Dec 2021 13:54:43: 19000000 INFO @ Sat, 11 Dec 2021 13:54:43: 29000000 INFO @ Sat, 11 Dec 2021 13:54:50: 16000000 INFO @ Sat, 11 Dec 2021 13:54:50: 30000000 INFO @ Sat, 11 Dec 2021 13:54:52: 20000000 INFO @ Sat, 11 Dec 2021 13:54:58: 31000000 INFO @ Sat, 11 Dec 2021 13:54:59: 17000000 INFO @ Sat, 11 Dec 2021 13:55:02: 21000000 INFO @ Sat, 11 Dec 2021 13:55:05: 32000000 INFO @ Sat, 11 Dec 2021 13:55:09: 18000000 INFO @ Sat, 11 Dec 2021 13:55:11: 33000000 INFO @ Sat, 11 Dec 2021 13:55:12: 22000000 INFO @ Sat, 11 Dec 2021 13:55:18: 34000000 INFO @ Sat, 11 Dec 2021 13:55:19: 19000000 INFO @ Sat, 11 Dec 2021 13:55:22: 23000000 INFO @ Sat, 11 Dec 2021 13:55:25: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:55:29: 20000000 INFO @ Sat, 11 Dec 2021 13:55:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:55:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:55:29: #1 total tags in treatment: 16784292 INFO @ Sat, 11 Dec 2021 13:55:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:55:29: #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 13:55:30: #1 tags after filtering in treatment: 13358272 INFO @ Sat, 11 Dec 2021 13:55:30: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 13:55:30: #1 finished! INFO @ Sat, 11 Dec 2021 13:55:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:55:31: #2 number of paired peaks: 288 WARNING @ Sat, 11 Dec 2021 13:55:31: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sat, 11 Dec 2021 13:55:31: start model_add_line... INFO @ Sat, 11 Dec 2021 13:55:31: start X-correlation... INFO @ Sat, 11 Dec 2021 13:55:31: end of X-cor INFO @ Sat, 11 Dec 2021 13:55:31: #2 finished! INFO @ Sat, 11 Dec 2021 13:55:31: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 13:55:31: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Dec 2021 13:55:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.05_model.r INFO @ Sat, 11 Dec 2021 13:55:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:55:32: 24000000 INFO @ Sat, 11 Dec 2021 13:55:39: 21000000 INFO @ Sat, 11 Dec 2021 13:55:41: 25000000 INFO @ Sat, 11 Dec 2021 13:55:49: 22000000 INFO @ Sat, 11 Dec 2021 13:55:50: 26000000 INFO @ Sat, 11 Dec 2021 13:55:58: 23000000 INFO @ Sat, 11 Dec 2021 13:56:00: 27000000 INFO @ Sat, 11 Dec 2021 13:56:08: 24000000 INFO @ Sat, 11 Dec 2021 13:56:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:56:09: 28000000 INFO @ Sat, 11 Dec 2021 13:56:17: 25000000 INFO @ Sat, 11 Dec 2021 13:56:18: 29000000 INFO @ Sat, 11 Dec 2021 13:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.05_summits.bed INFO @ Sat, 11 Dec 2021 13:56:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1809 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:56:26: 26000000 INFO @ Sat, 11 Dec 2021 13:56:27: 30000000 INFO @ Sat, 11 Dec 2021 13:56:36: 31000000 INFO @ Sat, 11 Dec 2021 13:56:36: 27000000 INFO @ Sat, 11 Dec 2021 13:56:44: 32000000 INFO @ Sat, 11 Dec 2021 13:56:45: 28000000 INFO @ Sat, 11 Dec 2021 13:56:52: 33000000 INFO @ Sat, 11 Dec 2021 13:56:55: 29000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:57:00: 34000000 INFO @ Sat, 11 Dec 2021 13:57:04: 30000000 INFO @ Sat, 11 Dec 2021 13:57:09: 35000000 INFO @ Sat, 11 Dec 2021 13:57:13: 31000000 INFO @ Sat, 11 Dec 2021 13:57:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:57:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:57:14: #1 total tags in treatment: 16784292 INFO @ Sat, 11 Dec 2021 13:57:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:57:14: #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 13:57:14: #1 tags after filtering in treatment: 13358272 INFO @ Sat, 11 Dec 2021 13:57:14: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 13:57:14: #1 finished! INFO @ Sat, 11 Dec 2021 13:57:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:57:15: #2 number of paired peaks: 288 WARNING @ Sat, 11 Dec 2021 13:57:15: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sat, 11 Dec 2021 13:57:15: start model_add_line... INFO @ Sat, 11 Dec 2021 13:57:15: start X-correlation... INFO @ Sat, 11 Dec 2021 13:57:15: end of X-cor INFO @ Sat, 11 Dec 2021 13:57:15: #2 finished! INFO @ Sat, 11 Dec 2021 13:57:15: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 13:57:15: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Dec 2021 13:57:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.10_model.r INFO @ Sat, 11 Dec 2021 13:57:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:57:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:57:21: 32000000 INFO @ Sat, 11 Dec 2021 13:57:29: 33000000 INFO @ Sat, 11 Dec 2021 13:57:37: 34000000 INFO @ Sat, 11 Dec 2021 13:57:45: 35000000 INFO @ Sat, 11 Dec 2021 13:57:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:57:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:57:50: #1 total tags in treatment: 16784292 INFO @ Sat, 11 Dec 2021 13:57:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:57:50: #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 13:57:50: #1 tags after filtering in treatment: 13358272 INFO @ Sat, 11 Dec 2021 13:57:50: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 13:57:50: #1 finished! INFO @ Sat, 11 Dec 2021 13:57:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:57:51: #2 number of paired peaks: 288 WARNING @ Sat, 11 Dec 2021 13:57:51: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Sat, 11 Dec 2021 13:57:51: start model_add_line... INFO @ Sat, 11 Dec 2021 13:57:52: start X-correlation... INFO @ Sat, 11 Dec 2021 13:57:52: end of X-cor INFO @ Sat, 11 Dec 2021 13:57:52: #2 finished! INFO @ Sat, 11 Dec 2021 13:57:52: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 13:57:52: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Dec 2021 13:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.20_model.r INFO @ Sat, 11 Dec 2021 13:57:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:57:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.10_summits.bed INFO @ Sat, 11 Dec 2021 13:58:10: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1163 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:58:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:58:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:58:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:58:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386218/SRX10386218.20_summits.bed INFO @ Sat, 11 Dec 2021 13:58:46: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (818 records, 4 fields): 4 millis CompletedMACS2peakCalling