Job ID = 4178540 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:43:59 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 ) 2019-12-05T03:43:59 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.28' from '172.19.7.53' 2019-12-05T03:43:59 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' (130.14.250.28) from '172.19.7.53' 2019-12-05T03:43:59 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra33/SRR/008747/SRR8957001' 2019-12-05T03:43:59 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 ) 2019-12-05T03:43:59 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.28' from '172.19.7.53' 2019-12-05T03:43:59 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' (130.14.250.28) from '172.19.7.53' 2019-12-05T03:43:59 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra33/SRR/008747/SRR8957001' 2019-12-05T03:43:59 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 ) 2019-12-05T03:43:59 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.28' from '172.19.7.53' 2019-12-05T03:43:59 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' (130.14.250.28) from '172.19.7.53' 2019-12-05T03:43:59 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra33/SRR/008747/SRR8957001' 2019-12-05T03:44:09 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8957001' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-12-05T03:44:09 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8957001' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-12-05T03:44:09 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-12-05T03:44:09 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8957001' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-12-05T03:44:09 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-12-05T03:44:09 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 17,421,633 reads read : 17,421,633 reads written : 17,421,633 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: 00:05:34 17421633 reads; of these: 17421633 (100.00%) were unpaired; of these: 266669 (1.53%) aligned 0 times 14171782 (81.35%) aligned exactly 1 time 2983182 (17.12%) aligned >1 times 98.47% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5620558 / 17154964 = 0.3276 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:09:15: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:09:15: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:09:22: 1000000 INFO @ Thu, 05 Dec 2019 13:09:29: 2000000 INFO @ Thu, 05 Dec 2019 13:09:36: 3000000 INFO @ Thu, 05 Dec 2019 13:09:43: 4000000 INFO @ Thu, 05 Dec 2019 13:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:09:45: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:09:45: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:09:50: 5000000 INFO @ Thu, 05 Dec 2019 13:09:53: 1000000 INFO @ Thu, 05 Dec 2019 13:09:57: 6000000 INFO @ Thu, 05 Dec 2019 13:10:02: 2000000 INFO @ Thu, 05 Dec 2019 13:10:05: 7000000 INFO @ Thu, 05 Dec 2019 13:10:10: 3000000 INFO @ Thu, 05 Dec 2019 13:10:12: 8000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 05 Dec 2019 13:10:15: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:10:15: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:10:19: 4000000 INFO @ Thu, 05 Dec 2019 13:10:19: 9000000 INFO @ Thu, 05 Dec 2019 13:10:24: 1000000 INFO @ Thu, 05 Dec 2019 13:10:26: 10000000 INFO @ Thu, 05 Dec 2019 13:10:28: 5000000 INFO @ Thu, 05 Dec 2019 13:10:37: 2000000 INFO @ Thu, 05 Dec 2019 13:10:37: 11000000 INFO @ Thu, 05 Dec 2019 13:10:43: 6000000 INFO @ Thu, 05 Dec 2019 13:10:43: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:10:43: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:10:43: #1 total tags in treatment: 11534406 INFO @ Thu, 05 Dec 2019 13:10:43: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:10:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:10:44: #1 tags after filtering in treatment: 11534406 INFO @ Thu, 05 Dec 2019 13:10:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:10:44: #1 finished! INFO @ Thu, 05 Dec 2019 13:10:44: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:10:45: #2 number of paired peaks: 774 WARNING @ Thu, 05 Dec 2019 13:10:45: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Thu, 05 Dec 2019 13:10:45: start model_add_line... INFO @ Thu, 05 Dec 2019 13:10:46: start X-correlation... INFO @ Thu, 05 Dec 2019 13:10:46: end of X-cor INFO @ Thu, 05 Dec 2019 13:10:46: #2 finished! INFO @ Thu, 05 Dec 2019 13:10:46: #2 predicted fragment length is 0 bps INFO @ Thu, 05 Dec 2019 13:10:46: #2 alternative fragment length(s) may be 0,26,68,83,112,121,125,140,219,258,287,462,502,553 bps INFO @ Thu, 05 Dec 2019 13:10:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.05_model.r WARNING @ Thu, 05 Dec 2019 13:10:46: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:10:46: #2 You may need to consider one of the other alternative d(s): 0,26,68,83,112,121,125,140,219,258,287,462,502,553 WARNING @ Thu, 05 Dec 2019 13:10:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:10:46: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:10:49: 3000000 INFO @ Thu, 05 Dec 2019 13:10:53: 7000000 INFO @ Thu, 05 Dec 2019 13:10:57: 4000000 INFO @ Thu, 05 Dec 2019 13:11:01: 8000000 INFO @ Thu, 05 Dec 2019 13:11:05: 5000000 INFO @ Thu, 05 Dec 2019 13:11:09: 9000000 INFO @ Thu, 05 Dec 2019 13:11:13: 6000000 INFO @ Thu, 05 Dec 2019 13:11:17: 10000000 INFO @ Thu, 05 Dec 2019 13:11:23: 7000000 INFO @ Thu, 05 Dec 2019 13:11:27: 11000000 INFO @ Thu, 05 Dec 2019 13:11:31: 8000000 INFO @ Thu, 05 Dec 2019 13:11:31: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:11:31: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:11:31: #1 total tags in treatment: 11534406 INFO @ Thu, 05 Dec 2019 13:11:31: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:11:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:11:31: #1 tags after filtering in treatment: 11534406 INFO @ Thu, 05 Dec 2019 13:11:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:11:31: #1 finished! INFO @ Thu, 05 Dec 2019 13:11:31: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:11:32: #2 number of paired peaks: 774 WARNING @ Thu, 05 Dec 2019 13:11:32: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Thu, 05 Dec 2019 13:11:32: start model_add_line... INFO @ Thu, 05 Dec 2019 13:11:33: start X-correlation... INFO @ Thu, 05 Dec 2019 13:11:33: end of X-cor INFO @ Thu, 05 Dec 2019 13:11:33: #2 finished! INFO @ Thu, 05 Dec 2019 13:11:33: #2 predicted fragment length is 0 bps INFO @ Thu, 05 Dec 2019 13:11:33: #2 alternative fragment length(s) may be 0,26,68,83,112,121,125,140,219,258,287,462,502,553 bps INFO @ Thu, 05 Dec 2019 13:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.10_model.r WARNING @ Thu, 05 Dec 2019 13:11:33: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:11:33: #2 You may need to consider one of the other alternative d(s): 0,26,68,83,112,121,125,140,219,258,287,462,502,553 WARNING @ Thu, 05 Dec 2019 13:11:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:11:33: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:11:39: 9000000 INFO @ Thu, 05 Dec 2019 13:11:47: 10000000 INFO @ Thu, 05 Dec 2019 13:11:56: 11000000 INFO @ Thu, 05 Dec 2019 13:12:00: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:12:00: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:12:00: #1 total tags in treatment: 11534406 INFO @ Thu, 05 Dec 2019 13:12:00: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:12:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:12:00: #1 tags after filtering in treatment: 11534406 INFO @ Thu, 05 Dec 2019 13:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:12:00: #1 finished! INFO @ Thu, 05 Dec 2019 13:12:00: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:12:01: #2 number of paired peaks: 774 WARNING @ Thu, 05 Dec 2019 13:12:01: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Thu, 05 Dec 2019 13:12:01: start model_add_line... INFO @ Thu, 05 Dec 2019 13:12:02: start X-correlation... INFO @ Thu, 05 Dec 2019 13:12:02: end of X-cor INFO @ Thu, 05 Dec 2019 13:12:02: #2 finished! INFO @ Thu, 05 Dec 2019 13:12:02: #2 predicted fragment length is 0 bps INFO @ Thu, 05 Dec 2019 13:12:02: #2 alternative fragment length(s) may be 0,26,68,83,112,121,125,140,219,258,287,462,502,553 bps INFO @ Thu, 05 Dec 2019 13:12:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736591/SRX5736591.20_model.r WARNING @ Thu, 05 Dec 2019 13:12:02: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:12:02: #2 You may need to consider one of the other alternative d(s): 0,26,68,83,112,121,125,140,219,258,287,462,502,553 WARNING @ Thu, 05 Dec 2019 13:12:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:12:02: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:12:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 /var/spool/uge/at085/job_scripts/4178540: line 336: 9456 Terminated MACS $i /var/spool/uge/at085/job_scripts/4178540: line 336: 11121 Terminated MACS $i /var/spool/uge/at085/job_scripts/4178540: line 336: 13514 Terminated MACS $i ls: cannot access SRX5736591.05.bed: No such file or directory mv: cannot stat ‘SRX5736591.05.bed’: No such file or directory mv: cannot stat ‘SRX5736591.05.bb’: No such file or directory ls: cannot access SRX5736591.10.bed: No such file or directory mv: cannot stat ‘SRX5736591.10.bed’: No such file or directory mv: cannot stat ‘SRX5736591.10.bb’: No such file or directory ls: cannot access SRX5736591.20.bed: No such file or directory mv: cannot stat ‘SRX5736591.20.bed’: No such file or directory mv: cannot stat ‘SRX5736591.20.bb’: No such file or directory