Job ID = 2641121 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T12:22:24 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault 2019-08-24T12:32:37 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 : 10,345,450 reads read : 20,690,900 reads written : 20,690,900 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: 00:14:35 10345450 reads; of these: 10345450 (100.00%) were paired; of these: 5248476 (50.73%) aligned concordantly 0 times 4480677 (43.31%) aligned concordantly exactly 1 time 616297 (5.96%) aligned concordantly >1 times ---- 5248476 pairs aligned concordantly 0 times; of these: 3830921 (72.99%) aligned discordantly 1 time ---- 1417555 pairs aligned 0 times concordantly or discordantly; of these: 2835110 mates make up the pairs; of these: 1569078 (55.34%) aligned 0 times 155976 (5.50%) aligned exactly 1 time 1110056 (39.15%) aligned >1 times 92.42% overall alignment rate Time searching: 00:14:35 Overall time: 00:14:35 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 8 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] 488038 / 8926865 = 0.0547 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:07:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.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 @ Sat, 24 Aug 2019 22:07:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:07:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:07:18: 1000000 INFO @ Sat, 24 Aug 2019 22:07:27: 2000000 INFO @ Sat, 24 Aug 2019 22:07:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.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 @ Sat, 24 Aug 2019 22:07:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:07:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:07:37: 3000000 INFO @ Sat, 24 Aug 2019 22:07:42: 1000000 INFO @ Sat, 24 Aug 2019 22:07:46: 4000000 INFO @ Sat, 24 Aug 2019 22:07:51: 2000000 INFO @ Sat, 24 Aug 2019 22:07:56: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:08:00: 3000000 INFO @ Sat, 24 Aug 2019 22:08:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.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 @ Sat, 24 Aug 2019 22:08:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:06: 6000000 INFO @ Sat, 24 Aug 2019 22:08:09: 4000000 INFO @ Sat, 24 Aug 2019 22:08:13: 1000000 INFO @ Sat, 24 Aug 2019 22:08:16: 7000000 INFO @ Sat, 24 Aug 2019 22:08:19: 5000000 INFO @ Sat, 24 Aug 2019 22:08:23: 2000000 INFO @ Sat, 24 Aug 2019 22:08:25: 8000000 INFO @ Sat, 24 Aug 2019 22:08:28: 6000000 INFO @ Sat, 24 Aug 2019 22:08:33: 3000000 INFO @ Sat, 24 Aug 2019 22:08:35: 9000000 INFO @ Sat, 24 Aug 2019 22:08:38: 7000000 INFO @ Sat, 24 Aug 2019 22:08:44: 4000000 INFO @ Sat, 24 Aug 2019 22:08:45: 10000000 INFO @ Sat, 24 Aug 2019 22:08:47: 8000000 INFO @ Sat, 24 Aug 2019 22:08:54: 11000000 INFO @ Sat, 24 Aug 2019 22:08:55: 5000000 INFO @ Sat, 24 Aug 2019 22:08:57: 9000000 INFO @ Sat, 24 Aug 2019 22:09:03: 12000000 INFO @ Sat, 24 Aug 2019 22:09:05: 6000000 INFO @ Sat, 24 Aug 2019 22:09:06: 10000000 INFO @ Sat, 24 Aug 2019 22:09:13: 13000000 INFO @ Sat, 24 Aug 2019 22:09:15: 11000000 INFO @ Sat, 24 Aug 2019 22:09:16: 7000000 INFO @ Sat, 24 Aug 2019 22:09:22: 14000000 INFO @ Sat, 24 Aug 2019 22:09:25: 12000000 INFO @ Sat, 24 Aug 2019 22:09:26: 8000000 INFO @ Sat, 24 Aug 2019 22:09:32: 15000000 INFO @ Sat, 24 Aug 2019 22:09:34: 13000000 INFO @ Sat, 24 Aug 2019 22:09:37: 9000000 INFO @ Sat, 24 Aug 2019 22:09:41: 16000000 INFO @ Sat, 24 Aug 2019 22:09:44: 14000000 INFO @ Sat, 24 Aug 2019 22:09:48: 10000000 INFO @ Sat, 24 Aug 2019 22:09:51: 17000000 INFO @ Sat, 24 Aug 2019 22:09:53: 15000000 INFO @ Sat, 24 Aug 2019 22:09:58: 11000000 INFO @ Sat, 24 Aug 2019 22:10:00: 18000000 INFO @ Sat, 24 Aug 2019 22:10:02: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:10:02: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:10:02: #1 total tags in treatment: 4805497 INFO @ Sat, 24 Aug 2019 22:10:02: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:10:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:10:02: #1 tags after filtering in treatment: 3928376 INFO @ Sat, 24 Aug 2019 22:10:02: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 24 Aug 2019 22:10:02: #1 finished! INFO @ Sat, 24 Aug 2019 22:10:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:10:02: 16000000 INFO @ Sat, 24 Aug 2019 22:10:02: #2 number of paired peaks: 159 WARNING @ Sat, 24 Aug 2019 22:10:02: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 24 Aug 2019 22:10:02: start model_add_line... INFO @ Sat, 24 Aug 2019 22:10:02: start X-correlation... INFO @ Sat, 24 Aug 2019 22:10:02: end of X-cor INFO @ Sat, 24 Aug 2019 22:10:02: #2 finished! INFO @ Sat, 24 Aug 2019 22:10:02: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:10:02: #2 alternative fragment length(s) may be 0,38,70,85,90,112,130,138,166,195,225,252,259,275,293,310,330,339,342,367,372,399,431,444,462,494,512,537,547,551,571,595 bps INFO @ Sat, 24 Aug 2019 22:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.05_model.r WARNING @ Sat, 24 Aug 2019 22:10:02: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 22:10:02: #2 You may need to consider one of the other alternative d(s): 0,38,70,85,90,112,130,138,166,195,225,252,259,275,293,310,330,339,342,367,372,399,431,444,462,494,512,537,547,551,571,595 WARNING @ Sat, 24 Aug 2019 22:10:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 22:10:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:10:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:10:09: 12000000 INFO @ Sat, 24 Aug 2019 22:10:11: 17000000 INFO @ Sat, 24 Aug 2019 22:10:19: 13000000 INFO @ Sat, 24 Aug 2019 22:10:20: 18000000 INFO @ Sat, 24 Aug 2019 22:10:22: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:10:22: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:10:22: #1 total tags in treatment: 4805497 INFO @ Sat, 24 Aug 2019 22:10:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:10:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:10:22: #1 tags after filtering in treatment: 3928376 INFO @ Sat, 24 Aug 2019 22:10:22: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 24 Aug 2019 22:10:22: #1 finished! INFO @ Sat, 24 Aug 2019 22:10:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:10:22: #2 number of paired peaks: 159 WARNING @ Sat, 24 Aug 2019 22:10:22: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 24 Aug 2019 22:10:22: start model_add_line... INFO @ Sat, 24 Aug 2019 22:10:22: start X-correlation... INFO @ Sat, 24 Aug 2019 22:10:22: end of X-cor INFO @ Sat, 24 Aug 2019 22:10:22: #2 finished! INFO @ Sat, 24 Aug 2019 22:10:22: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:10:22: #2 alternative fragment length(s) may be 0,38,70,85,90,112,130,138,166,195,225,252,259,275,293,310,330,339,342,367,372,399,431,444,462,494,512,537,547,551,571,595 bps INFO @ Sat, 24 Aug 2019 22:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546560/SRX5546560.10_model.r WARNING @ Sat, 24 Aug 2019 22:10:22: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 22:10:22: #2 You may need to consider one of the other alternative d(s): 0,38,70,85,90,112,130,138,166,195,225,252,259,275,293,310,330,339,342,367,372,399,431,444,462,494,512,537,547,551,571,595 WARNING @ Sat, 24 Aug 2019 22:10:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 22:10:22: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:10:29: 14000000 INFO @ Sat, 24 Aug 2019 22:10:39: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:10:49: 16000000 INFO @ Sat, 24 Aug 2019 22:10:59: 17000000 BigWig に変換しました。 /var/spool/uge/at083/job_scripts/2641121: line 336: 1851 Terminated MACS $i /var/spool/uge/at083/job_scripts/2641121: line 336: 1965 Terminated MACS $i /var/spool/uge/at083/job_scripts/2641121: line 336: 2100 Terminated MACS $i ls: cannot access SRX5546560.05.bed: No such file or directory mv: cannot stat ‘SRX5546560.05.bed’: No such file or directory mv: cannot stat ‘SRX5546560.05.bb’: No such file or directory ls: cannot access SRX5546560.10.bed: No such file or directory mv: cannot stat ‘SRX5546560.10.bed’: No such file or directory mv: cannot stat ‘SRX5546560.10.bb’: No such file or directory ls: cannot access SRX5546560.20.bed: No such file or directory mv: cannot stat ‘SRX5546560.20.bed’: No such file or directory mv: cannot stat ‘SRX5546560.20.bb’: No such file or directory