Job ID = 2010526 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:05:02 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 ) 2019-07-05T14:05:02 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 ) 2019-07-05T14:05:02 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 : 15,134,681 reads read : 30,269,362 reads written : 30,269,362 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: 00:12:58 15134681 reads; of these: 15134681 (100.00%) were paired; of these: 1849952 (12.22%) aligned concordantly 0 times 10729039 (70.89%) aligned concordantly exactly 1 time 2555690 (16.89%) aligned concordantly >1 times ---- 1849952 pairs aligned concordantly 0 times; of these: 138238 (7.47%) aligned discordantly 1 time ---- 1711714 pairs aligned 0 times concordantly or discordantly; of these: 3423428 mates make up the pairs; of these: 3053532 (89.20%) aligned 0 times 217256 (6.35%) aligned exactly 1 time 152640 (4.46%) aligned >1 times 89.91% overall alignment rate Time searching: 00:12:58 Overall time: 00:12:58 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 12 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] 1954522 / 13408384 = 0.1458 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 23:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.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 23:29:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:29:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:29:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.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 23:29:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:29:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.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 23:29:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:29:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:30:03: 1000000 INFO @ Fri, 05 Jul 2019 23:30:04: 1000000 INFO @ Fri, 05 Jul 2019 23:30:08: 1000000 INFO @ Fri, 05 Jul 2019 23:30:13: 2000000 INFO @ Fri, 05 Jul 2019 23:30:14: 2000000 INFO @ Fri, 05 Jul 2019 23:30:20: 2000000 INFO @ Fri, 05 Jul 2019 23:30:22: 3000000 INFO @ Fri, 05 Jul 2019 23:30:23: 3000000 INFO @ Fri, 05 Jul 2019 23:30:31: 4000000 INFO @ Fri, 05 Jul 2019 23:30:32: 3000000 INFO @ Fri, 05 Jul 2019 23:30:32: 4000000 INFO @ Fri, 05 Jul 2019 23:30:40: 5000000 INFO @ Fri, 05 Jul 2019 23:30:42: 5000000 INFO @ Fri, 05 Jul 2019 23:30:43: 4000000 INFO @ Fri, 05 Jul 2019 23:30:49: 6000000 INFO @ Fri, 05 Jul 2019 23:30:51: 6000000 INFO @ Fri, 05 Jul 2019 23:30:54: 5000000 INFO @ Fri, 05 Jul 2019 23:30:58: 7000000 INFO @ Fri, 05 Jul 2019 23:31:00: 7000000 INFO @ Fri, 05 Jul 2019 23:31:05: 6000000 INFO @ Fri, 05 Jul 2019 23:31:07: 8000000 INFO @ Fri, 05 Jul 2019 23:31:10: 8000000 INFO @ Fri, 05 Jul 2019 23:31:16: 9000000 INFO @ Fri, 05 Jul 2019 23:31:16: 7000000 INFO @ Fri, 05 Jul 2019 23:31:19: 9000000 INFO @ Fri, 05 Jul 2019 23:31:25: 10000000 INFO @ Fri, 05 Jul 2019 23:31:27: 8000000 INFO @ Fri, 05 Jul 2019 23:31:28: 10000000 INFO @ Fri, 05 Jul 2019 23:31:35: 11000000 INFO @ Fri, 05 Jul 2019 23:31:38: 11000000 INFO @ Fri, 05 Jul 2019 23:31:38: 9000000 INFO @ Fri, 05 Jul 2019 23:31:43: 12000000 INFO @ Fri, 05 Jul 2019 23:31:48: 12000000 INFO @ Fri, 05 Jul 2019 23:31:49: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:31:52: 13000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:31:59: 13000000 INFO @ Fri, 05 Jul 2019 23:32:01: 11000000 INFO @ Fri, 05 Jul 2019 23:32:01: 14000000 INFO @ Fri, 05 Jul 2019 23:32:09: 14000000 INFO @ Fri, 05 Jul 2019 23:32:11: 15000000 INFO @ Fri, 05 Jul 2019 23:32:12: 12000000 INFO @ Fri, 05 Jul 2019 23:32:19: 15000000 INFO @ Fri, 05 Jul 2019 23:32:20: 16000000 INFO @ Fri, 05 Jul 2019 23:32:23: 13000000 INFO @ Fri, 05 Jul 2019 23:32:28: 16000000 INFO @ Fri, 05 Jul 2019 23:32:29: 17000000 INFO @ Fri, 05 Jul 2019 23:32:34: 14000000 INFO @ Fri, 05 Jul 2019 23:32:38: 17000000 INFO @ Fri, 05 Jul 2019 23:32:39: 18000000 INFO @ Fri, 05 Jul 2019 23:32:45: 15000000 INFO @ Fri, 05 Jul 2019 23:32:47: 18000000 INFO @ Fri, 05 Jul 2019 23:32:48: 19000000 INFO @ Fri, 05 Jul 2019 23:32:56: 19000000 INFO @ Fri, 05 Jul 2019 23:32:56: 16000000 INFO @ Fri, 05 Jul 2019 23:32:57: 20000000 INFO @ Fri, 05 Jul 2019 23:33:05: 20000000 INFO @ Fri, 05 Jul 2019 23:33:06: 21000000 INFO @ Fri, 05 Jul 2019 23:33:09: 17000000 INFO @ Fri, 05 Jul 2019 23:33:14: 21000000 INFO @ Fri, 05 Jul 2019 23:33:15: 22000000 INFO @ Fri, 05 Jul 2019 23:33:21: 18000000 INFO @ Fri, 05 Jul 2019 23:33:23: 22000000 INFO @ Fri, 05 Jul 2019 23:33:24: 23000000 INFO @ Fri, 05 Jul 2019 23:33:26: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:33:26: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:33:26: #1 total tags in treatment: 11336466 INFO @ Fri, 05 Jul 2019 23:33:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:33:26: #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 23:33:27: #1 tags after filtering in treatment: 2741856 INFO @ Fri, 05 Jul 2019 23:33:27: #1 Redundant rate of treatment: 0.76 INFO @ Fri, 05 Jul 2019 23:33:27: #1 finished! INFO @ Fri, 05 Jul 2019 23:33:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:33:27: #2 number of paired peaks: 1432 INFO @ Fri, 05 Jul 2019 23:33:27: start model_add_line... INFO @ Fri, 05 Jul 2019 23:33:27: start X-correlation... INFO @ Fri, 05 Jul 2019 23:33:27: end of X-cor INFO @ Fri, 05 Jul 2019 23:33:27: #2 finished! INFO @ Fri, 05 Jul 2019 23:33:27: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:33:27: #2 alternative fragment length(s) may be 0,21,62,79,109,138,193,460,492,522,550,598 bps INFO @ Fri, 05 Jul 2019 23:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381229/SRX381229.05_model.r WARNING @ Fri, 05 Jul 2019 23:33:31: #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 23:33:31: #2 You may need to consider one of the other alternative d(s): 0,21,62,79,109,138,193,460,492,522,550,598 WARNING @ Fri, 05 Jul 2019 23:33:31: #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 23:33:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:33:31: #3 Pre-compute pvalue-qvalue table... ls: cannot access SRX381229.05.bed: No such file or directory mv: cannot stat ‘SRX381229.05.bed’: No such file or directory /var/spool/uge/at080/job_scripts/2010526: line 335: 54841 Terminated MACS $i /var/spool/uge/at080/job_scripts/2010526: line 335: 54856 Terminated MACS $i /var/spool/uge/at080/job_scripts/2010526: line 335: 54870 Terminated MACS $i mv: cannot stat ‘SRX381229.05.bb’: No such file or directory ls: cannot access SRX381229.10.bed: No such file or directory mv: cannot stat ‘SRX381229.10.bed’: No such file or directory mv: cannot stat ‘SRX381229.10.bb’: No such file or directory ls: cannot access SRX381229.20.bed: No such file or directory mv: cannot stat ‘SRX381229.20.bed’: No such file or directory mv: cannot stat ‘SRX381229.20.bb’: No such file or directory