Job ID = 2010585 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:21:50 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 ) 2019-07-05T14:21:50 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 ) 2019-07-05T14:24:21 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 ) 2019-07-05T14:24:21 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 ) 2019-07-05T14:24:56 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T14:24:56 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.24' from '172.19.7.49' 2019-07-05T14:24:56 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.24) from '172.19.7.49' spots read : 5,500,332 reads read : 11,000,664 reads written : 11,000,664 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: 00:03:30 5500332 reads; of these: 5500332 (100.00%) were paired; of these: 1724228 (31.35%) aligned concordantly 0 times 3397866 (61.78%) aligned concordantly exactly 1 time 378238 (6.88%) aligned concordantly >1 times ---- 1724228 pairs aligned concordantly 0 times; of these: 40416 (2.34%) aligned discordantly 1 time ---- 1683812 pairs aligned 0 times concordantly or discordantly; of these: 3367624 mates make up the pairs; of these: 3204631 (95.16%) aligned 0 times 114931 (3.41%) aligned exactly 1 time 48062 (1.43%) aligned >1 times 70.87% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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_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] 281289 / 3813610 = 0.0738 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 23:35:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.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 23:35:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:35:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:35:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.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 23:35:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:35:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.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 23:35:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:35:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:35:29: 1000000 INFO @ Fri, 05 Jul 2019 23:35:29: 1000000 INFO @ Fri, 05 Jul 2019 23:35:32: 1000000 INFO @ Fri, 05 Jul 2019 23:35:35: 2000000 INFO @ Fri, 05 Jul 2019 23:35:37: 2000000 INFO @ Fri, 05 Jul 2019 23:35:40: 2000000 INFO @ Fri, 05 Jul 2019 23:35:41: 3000000 INFO @ Fri, 05 Jul 2019 23:35:45: 3000000 INFO @ Fri, 05 Jul 2019 23:35:48: 4000000 INFO @ Fri, 05 Jul 2019 23:35:49: 3000000 INFO @ Fri, 05 Jul 2019 23:35:53: 4000000 INFO @ Fri, 05 Jul 2019 23:35:54: 5000000 INFO @ Fri, 05 Jul 2019 23:35:58: 4000000 INFO @ Fri, 05 Jul 2019 23:36:00: 6000000 INFO @ Fri, 05 Jul 2019 23:36:01: 5000000 INFO @ Fri, 05 Jul 2019 23:36:06: 5000000 INFO @ Fri, 05 Jul 2019 23:36:07: 7000000 INFO @ Fri, 05 Jul 2019 23:36:09: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:36:09: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:36:09: #1 total tags in treatment: 3496478 INFO @ Fri, 05 Jul 2019 23:36:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:36:09: #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 23:36:09: #1 tags after filtering in treatment: 1403261 INFO @ Fri, 05 Jul 2019 23:36:09: #1 Redundant rate of treatment: 0.60 INFO @ Fri, 05 Jul 2019 23:36:09: #1 finished! INFO @ Fri, 05 Jul 2019 23:36:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:36:09: 6000000 INFO @ Fri, 05 Jul 2019 23:36:09: #2 number of paired peaks: 213 WARNING @ Fri, 05 Jul 2019 23:36:09: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Fri, 05 Jul 2019 23:36:09: start model_add_line... INFO @ Fri, 05 Jul 2019 23:36:09: start X-correlation... INFO @ Fri, 05 Jul 2019 23:36:09: end of X-cor INFO @ Fri, 05 Jul 2019 23:36:09: #2 finished! INFO @ Fri, 05 Jul 2019 23:36:09: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:36:09: #2 alternative fragment length(s) may be 0,65,88,93,100,123,154,272,490,535,597 bps INFO @ Fri, 05 Jul 2019 23:36:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.10_model.r WARNING @ Fri, 05 Jul 2019 23:36:09: #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 23:36:09: #2 You may need to consider one of the other alternative d(s): 0,65,88,93,100,123,154,272,490,535,597 WARNING @ Fri, 05 Jul 2019 23:36:09: #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 23:36:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:36:15: 6000000 INFO @ Fri, 05 Jul 2019 23:36:17: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:36:18: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:36:18: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:36:18: #1 total tags in treatment: 3496478 INFO @ Fri, 05 Jul 2019 23:36:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:36:18: #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 23:36:19: #1 tags after filtering in treatment: 1403261 INFO @ Fri, 05 Jul 2019 23:36:19: #1 Redundant rate of treatment: 0.60 INFO @ Fri, 05 Jul 2019 23:36:19: #1 finished! INFO @ Fri, 05 Jul 2019 23:36:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:36:19: #2 number of paired peaks: 213 WARNING @ Fri, 05 Jul 2019 23:36:19: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Fri, 05 Jul 2019 23:36:19: start model_add_line... INFO @ Fri, 05 Jul 2019 23:36:19: start X-correlation... INFO @ Fri, 05 Jul 2019 23:36:19: end of X-cor INFO @ Fri, 05 Jul 2019 23:36:19: #2 finished! INFO @ Fri, 05 Jul 2019 23:36:19: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:36:19: #2 alternative fragment length(s) may be 0,65,88,93,100,123,154,272,490,535,597 bps INFO @ Fri, 05 Jul 2019 23:36:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381286/SRX381286.05_model.r WARNING @ Fri, 05 Jul 2019 23:36:19: #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 23:36:19: #2 You may need to consider one of the other alternative d(s): 0,65,88,93,100,123,154,272,490,535,597 WARNING @ Fri, 05 Jul 2019 23:36:19: #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 23:36:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:36:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:36:23: 7000000 BigWig に変換しました。 ls: cannot access SRX381286.05.bed: No such file or directory mv: cannot stat ‘SRX381286.05.bed’: No such file or directory /var/spool/uge/at081/job_scripts/2010585: line 335: 41236 Terminated MACS $i /var/spool/uge/at081/job_scripts/2010585: line 335: 41252 Terminated MACS $i /var/spool/uge/at081/job_scripts/2010585: line 335: 41268 Terminated MACS $i mv: cannot stat ‘SRX381286.05.bb’: No such file or directory ls: cannot access SRX381286.10.bed: No such file or directory mv: cannot stat ‘SRX381286.10.bed’: No such file or directory mv: cannot stat ‘SRX381286.10.bb’: No such file or directory ls: cannot access SRX381286.20.bed: No such file or directory mv: cannot stat ‘SRX381286.20.bed’: No such file or directory mv: cannot stat ‘SRX381286.20.bb’: No such file or directory INFO @ Fri, 05 Jul 2019 23:36:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:36:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:36:25: #1 total tags in treatment: 3496478 INFO @ Fri, 05 Jul 2019 23:36:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:36:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s)