Job ID = 1294524 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:39:38 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 ) 2019-06-02T23:39:38 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 ) 2019-06-02T23:39:38 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 ) 2019-06-02T23:40:01 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 ) 2019-06-02T23:40:01 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 ) 2019-06-02T23:40:01 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 ) 2019-06-02T23:43:18 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 ) 2019-06-02T23:44:16 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 : 17,853,523 reads read : 17,853,523 reads written : 17,853,523 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: 00:06:56 17853523 reads; of these: 17853523 (100.00%) were unpaired; of these: 1106242 (6.20%) aligned 0 times 13214608 (74.02%) aligned exactly 1 time 3532673 (19.79%) aligned >1 times 93.80% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 1313187 / 16747281 = 0.0784 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 09:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.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 09:01:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:01:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.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 09:01:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:01:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.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 09:01:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:01:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:01:42: 1000000 INFO @ Mon, 03 Jun 2019 09:01:42: 1000000 INFO @ Mon, 03 Jun 2019 09:01:43: 1000000 INFO @ Mon, 03 Jun 2019 09:01:51: 2000000 INFO @ Mon, 03 Jun 2019 09:01:51: 2000000 INFO @ Mon, 03 Jun 2019 09:01:52: 2000000 INFO @ Mon, 03 Jun 2019 09:01:59: 3000000 INFO @ Mon, 03 Jun 2019 09:01:59: 3000000 INFO @ Mon, 03 Jun 2019 09:02:01: 3000000 INFO @ Mon, 03 Jun 2019 09:02:07: 4000000 INFO @ Mon, 03 Jun 2019 09:02:07: 4000000 INFO @ Mon, 03 Jun 2019 09:02:10: 4000000 INFO @ Mon, 03 Jun 2019 09:02:16: 5000000 INFO @ Mon, 03 Jun 2019 09:02:16: 5000000 INFO @ Mon, 03 Jun 2019 09:02:19: 5000000 INFO @ Mon, 03 Jun 2019 09:02:24: 6000000 INFO @ Mon, 03 Jun 2019 09:02:24: 6000000 INFO @ Mon, 03 Jun 2019 09:02:28: 6000000 INFO @ Mon, 03 Jun 2019 09:02:32: 7000000 INFO @ Mon, 03 Jun 2019 09:02:33: 7000000 INFO @ Mon, 03 Jun 2019 09:02:36: 7000000 INFO @ Mon, 03 Jun 2019 09:02:41: 8000000 INFO @ Mon, 03 Jun 2019 09:02:41: 8000000 INFO @ Mon, 03 Jun 2019 09:02:45: 8000000 INFO @ Mon, 03 Jun 2019 09:02:49: 9000000 INFO @ Mon, 03 Jun 2019 09:02:49: 9000000 INFO @ Mon, 03 Jun 2019 09:02:54: 9000000 INFO @ Mon, 03 Jun 2019 09:02:57: 10000000 INFO @ Mon, 03 Jun 2019 09:02:58: 10000000 INFO @ Mon, 03 Jun 2019 09:03:03: 10000000 INFO @ Mon, 03 Jun 2019 09:03:06: 11000000 INFO @ Mon, 03 Jun 2019 09:03:06: 11000000 INFO @ Mon, 03 Jun 2019 09:03:12: 11000000 INFO @ Mon, 03 Jun 2019 09:03:14: 12000000 INFO @ Mon, 03 Jun 2019 09:03:14: 12000000 INFO @ Mon, 03 Jun 2019 09:03:20: 12000000 INFO @ Mon, 03 Jun 2019 09:03:22: 13000000 INFO @ Mon, 03 Jun 2019 09:03:23: 13000000 INFO @ Mon, 03 Jun 2019 09:03:29: 13000000 INFO @ Mon, 03 Jun 2019 09:03:31: 14000000 INFO @ Mon, 03 Jun 2019 09:03:31: 14000000 INFO @ Mon, 03 Jun 2019 09:03:37: 14000000 INFO @ Mon, 03 Jun 2019 09:03:39: 15000000 INFO @ Mon, 03 Jun 2019 09:03:39: 15000000 INFO @ Mon, 03 Jun 2019 09:03:43: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:03:43: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:03:43: #1 total tags in treatment: 15434094 INFO @ Mon, 03 Jun 2019 09:03:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:03:43: #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 09:03:43: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:03:43: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:03:43: #1 total tags in treatment: 15434094 INFO @ Mon, 03 Jun 2019 09:03:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:03:43: #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 09:03:43: #1 tags after filtering in treatment: 15434094 INFO @ Mon, 03 Jun 2019 09:03:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:03:43: #1 finished! INFO @ Mon, 03 Jun 2019 09:03:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:03:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:03:43: #1 tags after filtering in treatment: 15434094 INFO @ Mon, 03 Jun 2019 09:03:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:03:43: #1 finished! INFO @ Mon, 03 Jun 2019 09:03:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:03:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:03:44: #2 number of paired peaks: 121 WARNING @ Mon, 03 Jun 2019 09:03:44: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 03 Jun 2019 09:03:44: start model_add_line... INFO @ Mon, 03 Jun 2019 09:03:44: start X-correlation... INFO @ Mon, 03 Jun 2019 09:03:44: end of X-cor INFO @ Mon, 03 Jun 2019 09:03:44: #2 finished! INFO @ Mon, 03 Jun 2019 09:03:44: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:03:44: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:03:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.10_model.r WARNING @ Mon, 03 Jun 2019 09:03:44: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:03:44: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:03:44: #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 09:03:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:03:45: #2 number of paired peaks: 121 WARNING @ Mon, 03 Jun 2019 09:03:45: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 03 Jun 2019 09:03:45: start model_add_line... INFO @ Mon, 03 Jun 2019 09:03:45: start X-correlation... INFO @ Mon, 03 Jun 2019 09:03:45: end of X-cor INFO @ Mon, 03 Jun 2019 09:03:45: #2 finished! INFO @ Mon, 03 Jun 2019 09:03:45: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:03:45: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.20_model.r WARNING @ Mon, 03 Jun 2019 09:03:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:03:45: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:03:45: #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 09:03:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:03:46: 15000000 INFO @ Mon, 03 Jun 2019 09:03:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:03:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:03:50: #1 total tags in treatment: 15434094 INFO @ Mon, 03 Jun 2019 09:03:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:03:50: #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 09:03:50: #1 tags after filtering in treatment: 15434094 INFO @ Mon, 03 Jun 2019 09:03:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:03:50: #1 finished! INFO @ Mon, 03 Jun 2019 09:03:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:03:52: #2 number of paired peaks: 121 WARNING @ Mon, 03 Jun 2019 09:03:52: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 03 Jun 2019 09:03:52: start model_add_line... INFO @ Mon, 03 Jun 2019 09:03:52: start X-correlation... INFO @ Mon, 03 Jun 2019 09:03:52: end of X-cor INFO @ Mon, 03 Jun 2019 09:03:52: #2 finished! INFO @ Mon, 03 Jun 2019 09:03:52: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:03:52: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.05_model.r WARNING @ Mon, 03 Jun 2019 09:03:52: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:03:52: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:03:52: #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 09:03:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:04:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:04:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:04:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.20_summits.bed INFO @ Mon, 03 Jun 2019 09:04:50: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (803 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.10_summits.bed INFO @ Mon, 03 Jun 2019 09:04:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1393 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:04:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:04:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:04:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287718/SRX287718.05_summits.bed INFO @ Mon, 03 Jun 2019 09:04:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1826 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。