Job ID = 1293916 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T18:18:08 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 ) 2019-06-02T18:19:09 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 ) 2019-06-02T18:26:01 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T18:26:01 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR2984039/SRR2984039.1' 2019-06-02T18:26:01 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR2984039', 'SEQUENCE', 'CMP_READ' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T18:26:20 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T18:26:20 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR2984039/SRR2984039.1' 2019-06-02T18:26:20 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR2984039' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T18:26:20 fasterq-dump.2.9.6 err: perform_fastq_split_3_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T18:28:28 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 ) 2019-06-02T18:31:06 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T18:31:06 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/refseq/NC_000073.5' 2019-06-02T18:33:37 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 ) 2019-06-02T18:33:37 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 : 48,694,382 reads read : 48,694,382 reads written : 48,694,382 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:08:07 48694382 reads; of these: 48694382 (100.00%) were unpaired; of these: 36637607 (75.24%) aligned 0 times 8479039 (17.41%) aligned exactly 1 time 3577736 (7.35%) aligned >1 times 24.76% overall alignment rate Time searching: 00:08:07 Overall time: 00:08:07 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] 2713974 / 12056775 = 0.2251 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 @ Mon, 03 Jun 2019 04:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.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 @ Mon, 03 Jun 2019 04:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.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 @ Mon, 03 Jun 2019 04:04:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:04:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:04:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:04:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.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 @ Mon, 03 Jun 2019 04:04:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:04:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:04:34: 1000000 INFO @ Mon, 03 Jun 2019 04:04:34: 1000000 INFO @ Mon, 03 Jun 2019 04:04:36: 1000000 INFO @ Mon, 03 Jun 2019 04:04:41: 2000000 INFO @ Mon, 03 Jun 2019 04:04:41: 2000000 INFO @ Mon, 03 Jun 2019 04:04:45: 2000000 INFO @ Mon, 03 Jun 2019 04:04:47: 3000000 INFO @ Mon, 03 Jun 2019 04:04:48: 3000000 INFO @ Mon, 03 Jun 2019 04:04:53: 3000000 INFO @ Mon, 03 Jun 2019 04:04:54: 4000000 INFO @ Mon, 03 Jun 2019 04:04:54: 4000000 INFO @ Mon, 03 Jun 2019 04:05:00: 5000000 INFO @ Mon, 03 Jun 2019 04:05:01: 5000000 INFO @ Mon, 03 Jun 2019 04:05:01: 4000000 INFO @ Mon, 03 Jun 2019 04:05:07: 6000000 INFO @ Mon, 03 Jun 2019 04:05:07: 6000000 INFO @ Mon, 03 Jun 2019 04:05:10: 5000000 INFO @ Mon, 03 Jun 2019 04:05:13: 7000000 INFO @ Mon, 03 Jun 2019 04:05:14: 7000000 INFO @ Mon, 03 Jun 2019 04:05:18: 6000000 INFO @ Mon, 03 Jun 2019 04:05:20: 8000000 INFO @ Mon, 03 Jun 2019 04:05:20: 8000000 INFO @ Mon, 03 Jun 2019 04:05:26: 9000000 INFO @ Mon, 03 Jun 2019 04:05:27: 7000000 INFO @ Mon, 03 Jun 2019 04:05:27: 9000000 INFO @ Mon, 03 Jun 2019 04:05:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:05:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:05:29: #1 total tags in treatment: 9342801 INFO @ Mon, 03 Jun 2019 04:05:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:05:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:05:29: #1 tags after filtering in treatment: 9342801 INFO @ Mon, 03 Jun 2019 04:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:05:29: #1 finished! INFO @ Mon, 03 Jun 2019 04:05:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:05:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:05:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:05:29: #1 total tags in treatment: 9342801 INFO @ Mon, 03 Jun 2019 04:05:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:05:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:05:29: #1 tags after filtering in treatment: 9342801 INFO @ Mon, 03 Jun 2019 04:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:05:29: #1 finished! INFO @ Mon, 03 Jun 2019 04:05:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:05:30: #2 number of paired peaks: 271 WARNING @ Mon, 03 Jun 2019 04:05:30: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 03 Jun 2019 04:05:30: start model_add_line... INFO @ Mon, 03 Jun 2019 04:05:30: start X-correlation... INFO @ Mon, 03 Jun 2019 04:05:30: end of X-cor INFO @ Mon, 03 Jun 2019 04:05:30: #2 finished! INFO @ Mon, 03 Jun 2019 04:05:30: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 04:05:30: #2 alternative fragment length(s) may be 3,45,81,500,521,543,568 bps INFO @ Mon, 03 Jun 2019 04:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.05_model.r WARNING @ Mon, 03 Jun 2019 04:05:30: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:05:30: #2 You may need to consider one of the other alternative d(s): 3,45,81,500,521,543,568 WARNING @ Mon, 03 Jun 2019 04:05:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 04:05:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:05:30: #2 number of paired peaks: 271 WARNING @ Mon, 03 Jun 2019 04:05:30: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 03 Jun 2019 04:05:30: start model_add_line... INFO @ Mon, 03 Jun 2019 04:05:30: start X-correlation... INFO @ Mon, 03 Jun 2019 04:05:30: end of X-cor INFO @ Mon, 03 Jun 2019 04:05:30: #2 finished! INFO @ Mon, 03 Jun 2019 04:05:30: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 04:05:30: #2 alternative fragment length(s) may be 3,45,81,500,521,543,568 bps INFO @ Mon, 03 Jun 2019 04:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.10_model.r WARNING @ Mon, 03 Jun 2019 04:05:30: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:05:30: #2 You may need to consider one of the other alternative d(s): 3,45,81,500,521,543,568 WARNING @ Mon, 03 Jun 2019 04:05:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 04:05:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:05:35: 8000000 INFO @ Mon, 03 Jun 2019 04:05:43: 9000000 INFO @ Mon, 03 Jun 2019 04:05:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:05:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:05:46: #1 total tags in treatment: 9342801 INFO @ Mon, 03 Jun 2019 04:05:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:05:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:05:46: #1 tags after filtering in treatment: 9342801 INFO @ Mon, 03 Jun 2019 04:05:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:05:46: #1 finished! INFO @ Mon, 03 Jun 2019 04:05:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:05:47: #2 number of paired peaks: 271 WARNING @ Mon, 03 Jun 2019 04:05:47: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 03 Jun 2019 04:05:47: start model_add_line... INFO @ Mon, 03 Jun 2019 04:05:47: start X-correlation... INFO @ Mon, 03 Jun 2019 04:05:47: end of X-cor INFO @ Mon, 03 Jun 2019 04:05:47: #2 finished! INFO @ Mon, 03 Jun 2019 04:05:47: #2 predicted fragment length is 81 bps INFO @ Mon, 03 Jun 2019 04:05:47: #2 alternative fragment length(s) may be 3,45,81,500,521,543,568 bps INFO @ Mon, 03 Jun 2019 04:05:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.20_model.r WARNING @ Mon, 03 Jun 2019 04:05:47: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:05:47: #2 You may need to consider one of the other alternative d(s): 3,45,81,500,521,543,568 WARNING @ Mon, 03 Jun 2019 04:05:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 04:05:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:05:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:05:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:05:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:06:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:06:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:06:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.05_summits.bed INFO @ Mon, 03 Jun 2019 04:06:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1931 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:06:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:06:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:06:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.10_summits.bed INFO @ Mon, 03 Jun 2019 04:06:09: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (754 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:06:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:06:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:06:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:06:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1473020/SRX1473020.20_summits.bed INFO @ Mon, 03 Jun 2019 04:06:28: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (219 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。