Job ID = 2010539 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 : 14,931,325 reads read : 29,862,650 reads written : 29,862,650 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: 00:12:28 14931325 reads; of these: 14931325 (100.00%) were paired; of these: 2826736 (18.93%) aligned concordantly 0 times 9734220 (65.19%) aligned concordantly exactly 1 time 2370369 (15.88%) aligned concordantly >1 times ---- 2826736 pairs aligned concordantly 0 times; of these: 214385 (7.58%) aligned discordantly 1 time ---- 2612351 pairs aligned 0 times concordantly or discordantly; of these: 5224702 mates make up the pairs; of these: 4749525 (90.91%) aligned 0 times 270780 (5.18%) aligned exactly 1 time 204397 (3.91%) aligned >1 times 84.10% overall alignment rate Time searching: 00:12:28 Overall time: 00:12:28 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] 1224422 / 12304941 = 0.0995 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 23:27:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.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 23:27:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:27:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:27:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.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 23:27:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:27:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:27:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.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 23:27:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:27:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:27:18: 1000000 INFO @ Fri, 05 Jul 2019 23:27:19: 1000000 INFO @ Fri, 05 Jul 2019 23:27:20: 1000000 INFO @ Fri, 05 Jul 2019 23:27:25: 2000000 INFO @ Fri, 05 Jul 2019 23:27:27: 2000000 INFO @ Fri, 05 Jul 2019 23:27:27: 2000000 INFO @ Fri, 05 Jul 2019 23:27:32: 3000000 INFO @ Fri, 05 Jul 2019 23:27:33: 3000000 INFO @ Fri, 05 Jul 2019 23:27:34: 3000000 INFO @ Fri, 05 Jul 2019 23:27:40: 4000000 INFO @ Fri, 05 Jul 2019 23:27:40: 4000000 INFO @ Fri, 05 Jul 2019 23:27:42: 4000000 INFO @ Fri, 05 Jul 2019 23:27:46: 5000000 INFO @ Fri, 05 Jul 2019 23:27:46: 5000000 INFO @ Fri, 05 Jul 2019 23:27:49: 5000000 INFO @ Fri, 05 Jul 2019 23:27:53: 6000000 INFO @ Fri, 05 Jul 2019 23:27:53: 6000000 INFO @ Fri, 05 Jul 2019 23:27:56: 6000000 INFO @ Fri, 05 Jul 2019 23:28:00: 7000000 INFO @ Fri, 05 Jul 2019 23:28:00: 7000000 INFO @ Fri, 05 Jul 2019 23:28:03: 7000000 INFO @ Fri, 05 Jul 2019 23:28:07: 8000000 INFO @ Fri, 05 Jul 2019 23:28:07: 8000000 INFO @ Fri, 05 Jul 2019 23:28:10: 8000000 INFO @ Fri, 05 Jul 2019 23:28:13: 9000000 INFO @ Fri, 05 Jul 2019 23:28:14: 9000000 INFO @ Fri, 05 Jul 2019 23:28:17: 9000000 INFO @ Fri, 05 Jul 2019 23:28:20: 10000000 INFO @ Fri, 05 Jul 2019 23:28:20: 10000000 INFO @ Fri, 05 Jul 2019 23:28:25: 10000000 INFO @ Fri, 05 Jul 2019 23:28:27: 11000000 INFO @ Fri, 05 Jul 2019 23:28:27: 11000000 INFO @ Fri, 05 Jul 2019 23:28:32: 11000000 INFO @ Fri, 05 Jul 2019 23:28:33: 12000000 INFO @ Fri, 05 Jul 2019 23:28:33: 12000000 INFO @ Fri, 05 Jul 2019 23:28:39: 12000000 INFO @ Fri, 05 Jul 2019 23:28:40: 13000000 INFO @ Fri, 05 Jul 2019 23:28:40: 13000000 INFO @ Fri, 05 Jul 2019 23:28:46: 13000000 INFO @ Fri, 05 Jul 2019 23:28:47: 14000000 INFO @ Fri, 05 Jul 2019 23:28:47: 14000000 INFO @ Fri, 05 Jul 2019 23:28:53: 15000000 INFO @ Fri, 05 Jul 2019 23:28:53: 14000000 INFO @ Fri, 05 Jul 2019 23:28:54: 15000000 INFO @ Fri, 05 Jul 2019 23:28:59: 16000000 INFO @ Fri, 05 Jul 2019 23:29:00: 16000000 INFO @ Fri, 05 Jul 2019 23:29:00: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:29:06: 17000000 INFO @ Fri, 05 Jul 2019 23:29:07: 17000000 INFO @ Fri, 05 Jul 2019 23:29:07: 16000000 INFO @ Fri, 05 Jul 2019 23:29:14: 18000000 INFO @ Fri, 05 Jul 2019 23:29:14: 18000000 INFO @ Fri, 05 Jul 2019 23:29:15: 17000000 INFO @ Fri, 05 Jul 2019 23:29:21: 19000000 INFO @ Fri, 05 Jul 2019 23:29:21: 19000000 INFO @ Fri, 05 Jul 2019 23:29:22: 18000000 INFO @ Fri, 05 Jul 2019 23:29:29: 20000000 INFO @ Fri, 05 Jul 2019 23:29:29: 20000000 INFO @ Fri, 05 Jul 2019 23:29:29: 19000000 INFO @ Fri, 05 Jul 2019 23:29:36: 21000000 INFO @ Fri, 05 Jul 2019 23:29:36: 21000000 INFO @ Fri, 05 Jul 2019 23:29:36: 20000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:29:43: 22000000 INFO @ Fri, 05 Jul 2019 23:29:44: 22000000 INFO @ Fri, 05 Jul 2019 23:29:44: 21000000 INFO @ Fri, 05 Jul 2019 23:29:48: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:29:48: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:29:48: #1 total tags in treatment: 10887682 INFO @ Fri, 05 Jul 2019 23:29:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:29:48: #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 23:29:48: #1 tags after filtering in treatment: 3103978 INFO @ Fri, 05 Jul 2019 23:29:48: #1 Redundant rate of treatment: 0.71 INFO @ Fri, 05 Jul 2019 23:29:48: #1 finished! INFO @ Fri, 05 Jul 2019 23:29:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:29:48: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:29:48: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:29:48: #1 total tags in treatment: 10887682 INFO @ Fri, 05 Jul 2019 23:29:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:29:48: #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 23:29:49: #1 tags after filtering in treatment: 3103978 INFO @ Fri, 05 Jul 2019 23:29:49: #1 Redundant rate of treatment: 0.71 INFO @ Fri, 05 Jul 2019 23:29:49: #1 finished! INFO @ Fri, 05 Jul 2019 23:29:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:29:49: #2 number of paired peaks: 1397 INFO @ Fri, 05 Jul 2019 23:29:49: start model_add_line... INFO @ Fri, 05 Jul 2019 23:29:49: start X-correlation... INFO @ Fri, 05 Jul 2019 23:29:49: end of X-cor INFO @ Fri, 05 Jul 2019 23:29:49: #2 finished! INFO @ Fri, 05 Jul 2019 23:29:49: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:29:49: #2 alternative fragment length(s) may be 0,20,44,75,107,114,131,152,186,211,233,263,294,311,313,401,468,535,553,592 bps INFO @ Fri, 05 Jul 2019 23:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381241/SRX381241.20_model.r WARNING @ Fri, 05 Jul 2019 23:29:49: #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 23:29:49: #2 You may need to consider one of the other alternative d(s): 0,20,44,75,107,114,131,152,186,211,233,263,294,311,313,401,468,535,553,592 WARNING @ Fri, 05 Jul 2019 23:29:49: #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 23:29:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:29:49: #3 Pre-compute pvalue-qvalue table... ls: cannot access SRX381241.05.bed: No such file or directory mv: cannot stat ‘SRX381241.05.bed’: No such file or directory /var/spool/uge/at113/job_scripts/2010539: line 335: 60709 Terminated MACS $i /var/spool/uge/at113/job_scripts/2010539: line 335: 60724 Terminated MACS $i /var/spool/uge/at113/job_scripts/2010539: line 335: 60740 Terminated MACS $i mv: cannot stat ‘SRX381241.05.bb’: No such file or directory ls: cannot access SRX381241.10.bed: No such file or directory mv: cannot stat ‘SRX381241.10.bed’: No such file or directory mv: cannot stat ‘SRX381241.10.bb’: No such file or directory ls: cannot access SRX381241.20.bed: No such file or directory mv: cannot stat ‘SRX381241.20.bed’: No such file or directory mv: cannot stat ‘SRX381241.20.bb’: No such file or directory