Job ID = 2010543 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:02:36 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 16,034,451 reads read : 32,068,902 reads written : 32,068,902 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:05 16034451 reads; of these: 16034451 (100.00%) were paired; of these: 973032 (6.07%) aligned concordantly 0 times 12146498 (75.75%) aligned concordantly exactly 1 time 2914921 (18.18%) aligned concordantly >1 times ---- 973032 pairs aligned concordantly 0 times; of these: 144099 (14.81%) aligned discordantly 1 time ---- 828933 pairs aligned 0 times concordantly or discordantly; of these: 1657866 mates make up the pairs; of these: 1296220 (78.19%) aligned 0 times 215209 (12.98%) aligned exactly 1 time 146437 (8.83%) aligned >1 times 95.96% overall alignment rate Time searching: 00:15:05 Overall time: 00:15:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1576554 / 15191226 = 0.1038 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 23:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 05 Jul 2019 23:38:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:38:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:38:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 05 Jul 2019 23:38:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:38:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:38:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 05 Jul 2019 23:38:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:38:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:38:44: 1000000 INFO @ Fri, 05 Jul 2019 23:38:45: 1000000 INFO @ Fri, 05 Jul 2019 23:38:47: 1000000 INFO @ Fri, 05 Jul 2019 23:38:51: 2000000 INFO @ Fri, 05 Jul 2019 23:38:51: 2000000 INFO @ Fri, 05 Jul 2019 23:38:56: 2000000 INFO @ Fri, 05 Jul 2019 23:38:57: 3000000 INFO @ Fri, 05 Jul 2019 23:38:58: 3000000 INFO @ Fri, 05 Jul 2019 23:39:04: 3000000 INFO @ Fri, 05 Jul 2019 23:39:04: 4000000 INFO @ Fri, 05 Jul 2019 23:39:05: 4000000 INFO @ Fri, 05 Jul 2019 23:39:11: 5000000 INFO @ Fri, 05 Jul 2019 23:39:12: 5000000 INFO @ Fri, 05 Jul 2019 23:39:12: 4000000 INFO @ Fri, 05 Jul 2019 23:39:17: 6000000 INFO @ Fri, 05 Jul 2019 23:39:18: 6000000 INFO @ Fri, 05 Jul 2019 23:39:21: 5000000 INFO @ Fri, 05 Jul 2019 23:39:24: 7000000 INFO @ Fri, 05 Jul 2019 23:39:25: 7000000 INFO @ Fri, 05 Jul 2019 23:39:29: 6000000 INFO @ Fri, 05 Jul 2019 23:39:31: 8000000 INFO @ Fri, 05 Jul 2019 23:39:32: 8000000 INFO @ Fri, 05 Jul 2019 23:39:37: 9000000 INFO @ Fri, 05 Jul 2019 23:39:37: 7000000 INFO @ Fri, 05 Jul 2019 23:39:38: 9000000 INFO @ Fri, 05 Jul 2019 23:39:44: 10000000 INFO @ Fri, 05 Jul 2019 23:39:45: 10000000 INFO @ Fri, 05 Jul 2019 23:39:45: 8000000 INFO @ Fri, 05 Jul 2019 23:39:52: 11000000 INFO @ Fri, 05 Jul 2019 23:39:52: 11000000 INFO @ Fri, 05 Jul 2019 23:39:54: 9000000 INFO @ Fri, 05 Jul 2019 23:39:59: 12000000 INFO @ Fri, 05 Jul 2019 23:39:59: 12000000 INFO @ Fri, 05 Jul 2019 23:40:02: 10000000 INFO @ Fri, 05 Jul 2019 23:40:05: 13000000 INFO @ Fri, 05 Jul 2019 23:40:06: 13000000 INFO @ Fri, 05 Jul 2019 23:40:11: 11000000 INFO @ Fri, 05 Jul 2019 23:40:12: 14000000 INFO @ Fri, 05 Jul 2019 23:40:14: 14000000 INFO @ Fri, 05 Jul 2019 23:40:19: 12000000 INFO @ Fri, 05 Jul 2019 23:40:19: 15000000 INFO @ Fri, 05 Jul 2019 23:40:22: 15000000 INFO @ Fri, 05 Jul 2019 23:40:26: 16000000 INFO @ Fri, 05 Jul 2019 23:40:28: 13000000 INFO @ Fri, 05 Jul 2019 23:40:29: 16000000 INFO @ Fri, 05 Jul 2019 23:40:33: 17000000 INFO @ Fri, 05 Jul 2019 23:40:36: 14000000 INFO @ Fri, 05 Jul 2019 23:40:37: 17000000 INFO @ Fri, 05 Jul 2019 23:40:39: 18000000 INFO @ Fri, 05 Jul 2019 23:40:44: 18000000 INFO @ Fri, 05 Jul 2019 23:40:45: 15000000 INFO @ Fri, 05 Jul 2019 23:40:46: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:40:52: 19000000 INFO @ Fri, 05 Jul 2019 23:40:53: 20000000 INFO @ Fri, 05 Jul 2019 23:40:53: 16000000 INFO @ Fri, 05 Jul 2019 23:40:59: 20000000 INFO @ Fri, 05 Jul 2019 23:41:00: 21000000 INFO @ Fri, 05 Jul 2019 23:41:02: 17000000 INFO @ Fri, 05 Jul 2019 23:41:06: 21000000 INFO @ Fri, 05 Jul 2019 23:41:06: 22000000 INFO @ Fri, 05 Jul 2019 23:41:10: 18000000 INFO @ Fri, 05 Jul 2019 23:41:13: 23000000 INFO @ Fri, 05 Jul 2019 23:41:14: 22000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:41:19: 19000000 INFO @ Fri, 05 Jul 2019 23:41:20: 24000000 INFO @ Fri, 05 Jul 2019 23:41:21: 23000000 INFO @ Fri, 05 Jul 2019 23:41:27: 25000000 INFO @ Fri, 05 Jul 2019 23:41:27: 20000000 INFO @ Fri, 05 Jul 2019 23:41:28: 24000000 INFO @ Fri, 05 Jul 2019 23:41:35: 26000000 INFO @ Fri, 05 Jul 2019 23:41:35: 25000000 INFO @ Fri, 05 Jul 2019 23:41:36: 21000000 INFO @ Fri, 05 Jul 2019 23:41:42: 27000000 INFO @ Fri, 05 Jul 2019 23:41:42: 26000000 INFO @ Fri, 05 Jul 2019 23:41:44: 22000000 INFO @ Fri, 05 Jul 2019 23:41:46: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:41:46: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:41:46: #1 total tags in treatment: 13488076 INFO @ Fri, 05 Jul 2019 23:41:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:41:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:41:46: #1 tags after filtering in treatment: 3555956 INFO @ Fri, 05 Jul 2019 23:41:46: #1 Redundant rate of treatment: 0.74 INFO @ Fri, 05 Jul 2019 23:41:46: #1 finished! INFO @ Fri, 05 Jul 2019 23:41:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:41:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:41:47: #2 number of paired peaks: 1527 INFO @ Fri, 05 Jul 2019 23:41:47: start model_add_line... INFO @ Fri, 05 Jul 2019 23:41:47: start X-correlation... INFO @ Fri, 05 Jul 2019 23:41:47: end of X-cor INFO @ Fri, 05 Jul 2019 23:41:47: #2 finished! INFO @ Fri, 05 Jul 2019 23:41:47: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:41:47: #2 alternative fragment length(s) may be 0,18,42,60,83,107,136,154,176,200,235,258,288,378,506,531,590 bps INFO @ Fri, 05 Jul 2019 23:41:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381245/SRX381245.10_model.r WARNING @ Fri, 05 Jul 2019 23:41:47: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 23:41:47: #2 You may need to consider one of the other alternative d(s): 0,18,42,60,83,107,136,154,176,200,235,258,288,378,506,531,590 WARNING @ Fri, 05 Jul 2019 23:41:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:41:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:41:47: #3 Pre-compute pvalue-qvalue table... ls: cannot access SRX381245.05.bed: No such file or directory mv: cannot stat ‘SRX381245.05.bed’: No such file or directory /var/spool/uge/at114/job_scripts/2010543: line 335: 9959 Terminated MACS $i /var/spool/uge/at114/job_scripts/2010543: line 335: 9975 Terminated MACS $i /var/spool/uge/at114/job_scripts/2010543: line 335: 9989 Terminated MACS $i mv: cannot stat ‘SRX381245.05.bb’: No such file or directory ls: cannot access SRX381245.10.bed: No such file or directory mv: cannot stat ‘SRX381245.10.bed’: No such file or directory mv: cannot stat ‘SRX381245.10.bb’: No such file or directory ls: cannot access SRX381245.20.bed: No such file or directory mv: cannot stat ‘SRX381245.20.bed’: No such file or directory mv: cannot stat ‘SRX381245.20.bb’: No such file or directory