Job ID = 2589966 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:51:59 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 ) 2019-08-12T09:51:59 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 ) 2019-08-12T09:52:05 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 ) 2019-08-12T09:52:06 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 ) 2019-08-12T09:52:07 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 : 31,990,085 reads read : 31,990,085 reads written : 31,990,085 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163563.sra.cache’: 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: 00:10:40 31990085 reads; of these: 31990085 (100.00%) were unpaired; of these: 1352723 (4.23%) aligned 0 times 20560079 (64.27%) aligned exactly 1 time 10077283 (31.50%) aligned >1 times 95.77% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 14060139 / 30637362 = 0.4589 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, 12 Aug 2019 19:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:13:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:13:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:13:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:13:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 19:13:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:13:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:13:56: 1000000 INFO @ Mon, 12 Aug 2019 19:14:00: 1000000 INFO @ Mon, 12 Aug 2019 19:14:00: 1000000 INFO @ Mon, 12 Aug 2019 19:14:04: 2000000 INFO @ Mon, 12 Aug 2019 19:14:08: 2000000 INFO @ Mon, 12 Aug 2019 19:14:08: 2000000 INFO @ Mon, 12 Aug 2019 19:14:11: 3000000 INFO @ Mon, 12 Aug 2019 19:14:16: 3000000 INFO @ Mon, 12 Aug 2019 19:14:17: 3000000 INFO @ Mon, 12 Aug 2019 19:14:17: 4000000 INFO @ Mon, 12 Aug 2019 19:14:24: 5000000 INFO @ Mon, 12 Aug 2019 19:14:24: 4000000 INFO @ Mon, 12 Aug 2019 19:14:25: 4000000 INFO @ Mon, 12 Aug 2019 19:14:31: 6000000 INFO @ Mon, 12 Aug 2019 19:14:32: 5000000 INFO @ Mon, 12 Aug 2019 19:14:33: 5000000 INFO @ Mon, 12 Aug 2019 19:14:37: 7000000 INFO @ Mon, 12 Aug 2019 19:14:40: 6000000 INFO @ Mon, 12 Aug 2019 19:14:41: 6000000 INFO @ Mon, 12 Aug 2019 19:14:44: 8000000 INFO @ Mon, 12 Aug 2019 19:14:48: 7000000 INFO @ Mon, 12 Aug 2019 19:14:50: 7000000 INFO @ Mon, 12 Aug 2019 19:14:51: 9000000 INFO @ Mon, 12 Aug 2019 19:14:56: 8000000 INFO @ Mon, 12 Aug 2019 19:14:58: 10000000 INFO @ Mon, 12 Aug 2019 19:14:59: 8000000 INFO @ Mon, 12 Aug 2019 19:15:04: 9000000 INFO @ Mon, 12 Aug 2019 19:15:05: 11000000 INFO @ Mon, 12 Aug 2019 19:15:07: 9000000 INFO @ Mon, 12 Aug 2019 19:15:11: 10000000 INFO @ Mon, 12 Aug 2019 19:15:11: 12000000 INFO @ Mon, 12 Aug 2019 19:15:15: 10000000 INFO @ Mon, 12 Aug 2019 19:15:18: 13000000 INFO @ Mon, 12 Aug 2019 19:15:18: 11000000 INFO @ Mon, 12 Aug 2019 19:15:24: 11000000 INFO @ Mon, 12 Aug 2019 19:15:25: 14000000 INFO @ Mon, 12 Aug 2019 19:15:27: 12000000 INFO @ Mon, 12 Aug 2019 19:15:33: 15000000 INFO @ Mon, 12 Aug 2019 19:15:33: 12000000 INFO @ Mon, 12 Aug 2019 19:15:34: 13000000 INFO @ Mon, 12 Aug 2019 19:15:40: 16000000 INFO @ Mon, 12 Aug 2019 19:15:41: 13000000 INFO @ Mon, 12 Aug 2019 19:15:42: 14000000 INFO @ Mon, 12 Aug 2019 19:15:44: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:15:44: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:15:44: #1 total tags in treatment: 16577223 INFO @ Mon, 12 Aug 2019 19:15:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:15:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:15:44: #1 tags after filtering in treatment: 16577223 INFO @ Mon, 12 Aug 2019 19:15:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:15:44: #1 finished! INFO @ Mon, 12 Aug 2019 19:15:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:15:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:15:46: #2 number of paired peaks: 1238 INFO @ Mon, 12 Aug 2019 19:15:46: start model_add_line... INFO @ Mon, 12 Aug 2019 19:15:46: start X-correlation... INFO @ Mon, 12 Aug 2019 19:15:46: end of X-cor INFO @ Mon, 12 Aug 2019 19:15:46: #2 finished! INFO @ Mon, 12 Aug 2019 19:15:46: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 19:15:46: #2 alternative fragment length(s) may be 2,44 bps INFO @ Mon, 12 Aug 2019 19:15:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.05_model.r WARNING @ Mon, 12 Aug 2019 19:15:46: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:15:46: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Mon, 12 Aug 2019 19:15:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:15:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:15:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:15:49: 14000000 INFO @ Mon, 12 Aug 2019 19:15:50: 15000000 INFO @ Mon, 12 Aug 2019 19:15:58: 15000000 INFO @ Mon, 12 Aug 2019 19:15:58: 16000000 INFO @ Mon, 12 Aug 2019 19:16:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:16:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:16:02: #1 total tags in treatment: 16577223 INFO @ Mon, 12 Aug 2019 19:16:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:16:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:16:03: #1 tags after filtering in treatment: 16577223 INFO @ Mon, 12 Aug 2019 19:16:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:16:03: #1 finished! INFO @ Mon, 12 Aug 2019 19:16:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:16:04: #2 number of paired peaks: 1238 INFO @ Mon, 12 Aug 2019 19:16:04: start model_add_line... INFO @ Mon, 12 Aug 2019 19:16:05: start X-correlation... INFO @ Mon, 12 Aug 2019 19:16:05: end of X-cor INFO @ Mon, 12 Aug 2019 19:16:05: #2 finished! INFO @ Mon, 12 Aug 2019 19:16:05: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 19:16:05: #2 alternative fragment length(s) may be 2,44 bps INFO @ Mon, 12 Aug 2019 19:16:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.20_model.r WARNING @ Mon, 12 Aug 2019 19:16:05: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:16:05: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Mon, 12 Aug 2019 19:16:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:16:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:16:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:16:06: 16000000 INFO @ Mon, 12 Aug 2019 19:16:11: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:16:11: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:16:11: #1 total tags in treatment: 16577223 INFO @ Mon, 12 Aug 2019 19:16:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:16:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:16:11: #1 tags after filtering in treatment: 16577223 INFO @ Mon, 12 Aug 2019 19:16:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:16:11: #1 finished! INFO @ Mon, 12 Aug 2019 19:16:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:16:13: #2 number of paired peaks: 1238 INFO @ Mon, 12 Aug 2019 19:16:13: start model_add_line... INFO @ Mon, 12 Aug 2019 19:16:13: start X-correlation... INFO @ Mon, 12 Aug 2019 19:16:13: end of X-cor INFO @ Mon, 12 Aug 2019 19:16:13: #2 finished! INFO @ Mon, 12 Aug 2019 19:16:13: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 19:16:13: #2 alternative fragment length(s) may be 2,44 bps INFO @ Mon, 12 Aug 2019 19:16:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.10_model.r WARNING @ Mon, 12 Aug 2019 19:16:13: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:16:13: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Mon, 12 Aug 2019 19:16:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:16:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:16:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:16:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.05_summits.bed INFO @ Mon, 12 Aug 2019 19:16:41: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:16:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:16:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:16:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:16:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:16:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.20_summits.bed INFO @ Mon, 12 Aug 2019 19:16:59: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466497/SRX466497.10_summits.bed INFO @ Mon, 12 Aug 2019 19:17:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。