Job ID = 1293985 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-06-02T18:47:51 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 : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-06-02T18:55:23 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 : 3,926,626 reads read : 3,926,626 reads written : 3,926,626 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: 00:07:02 19926626 reads; of these: 19926626 (100.00%) were unpaired; of these: 1966052 (9.87%) aligned 0 times 14127956 (70.90%) aligned exactly 1 time 3832618 (19.23%) aligned >1 times 90.13% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 2082128 / 17960574 = 0.1159 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 04:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.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 04:08:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:08:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.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 04:08:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:08:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.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 04:08:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:08:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:08:49: 1000000 INFO @ Mon, 03 Jun 2019 04:08:49: 1000000 INFO @ Mon, 03 Jun 2019 04:08:51: 1000000 INFO @ Mon, 03 Jun 2019 04:08:56: 2000000 INFO @ Mon, 03 Jun 2019 04:08:57: 2000000 INFO @ Mon, 03 Jun 2019 04:09:00: 2000000 INFO @ Mon, 03 Jun 2019 04:09:04: 3000000 INFO @ Mon, 03 Jun 2019 04:09:04: 3000000 INFO @ Mon, 03 Jun 2019 04:09:08: 3000000 INFO @ Mon, 03 Jun 2019 04:09:11: 4000000 INFO @ Mon, 03 Jun 2019 04:09:12: 4000000 INFO @ Mon, 03 Jun 2019 04:09:17: 4000000 INFO @ Mon, 03 Jun 2019 04:09:18: 5000000 INFO @ Mon, 03 Jun 2019 04:09:20: 5000000 INFO @ Mon, 03 Jun 2019 04:09:26: 6000000 INFO @ Mon, 03 Jun 2019 04:09:27: 5000000 INFO @ Mon, 03 Jun 2019 04:09:28: 6000000 INFO @ Mon, 03 Jun 2019 04:09:34: 7000000 INFO @ Mon, 03 Jun 2019 04:09:35: 7000000 INFO @ Mon, 03 Jun 2019 04:09:36: 6000000 INFO @ Mon, 03 Jun 2019 04:09:41: 8000000 INFO @ Mon, 03 Jun 2019 04:09:43: 8000000 INFO @ Mon, 03 Jun 2019 04:09:45: 7000000 INFO @ Mon, 03 Jun 2019 04:09:47: 9000000 INFO @ Mon, 03 Jun 2019 04:09:50: 9000000 INFO @ Mon, 03 Jun 2019 04:09:53: 8000000 INFO @ Mon, 03 Jun 2019 04:09:55: 10000000 INFO @ Mon, 03 Jun 2019 04:09:57: 10000000 INFO @ Mon, 03 Jun 2019 04:10:01: 9000000 INFO @ Mon, 03 Jun 2019 04:10:02: 11000000 INFO @ Mon, 03 Jun 2019 04:10:04: 11000000 INFO @ Mon, 03 Jun 2019 04:10:09: 12000000 INFO @ Mon, 03 Jun 2019 04:10:09: 10000000 INFO @ Mon, 03 Jun 2019 04:10:12: 12000000 INFO @ Mon, 03 Jun 2019 04:10:16: 13000000 INFO @ Mon, 03 Jun 2019 04:10:18: 11000000 INFO @ Mon, 03 Jun 2019 04:10:20: 13000000 INFO @ Mon, 03 Jun 2019 04:10:23: 14000000 INFO @ Mon, 03 Jun 2019 04:10:26: 12000000 INFO @ Mon, 03 Jun 2019 04:10:27: 14000000 INFO @ Mon, 03 Jun 2019 04:10:30: 15000000 INFO @ Mon, 03 Jun 2019 04:10:34: 13000000 INFO @ Mon, 03 Jun 2019 04:10:35: 15000000 INFO @ Mon, 03 Jun 2019 04:10:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:10:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:10:37: #1 total tags in treatment: 15878446 INFO @ Mon, 03 Jun 2019 04:10:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:10:37: #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 04:10:37: #1 tags after filtering in treatment: 15878446 INFO @ Mon, 03 Jun 2019 04:10:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:10:37: #1 finished! INFO @ Mon, 03 Jun 2019 04:10:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:10:39: #2 number of paired peaks: 113 WARNING @ Mon, 03 Jun 2019 04:10:39: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 03 Jun 2019 04:10:39: start model_add_line... INFO @ Mon, 03 Jun 2019 04:10:39: start X-correlation... INFO @ Mon, 03 Jun 2019 04:10:39: end of X-cor INFO @ Mon, 03 Jun 2019 04:10:39: #2 finished! INFO @ Mon, 03 Jun 2019 04:10:39: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 04:10:39: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 04:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.10_model.r WARNING @ Mon, 03 Jun 2019 04:10:39: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:10:39: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 04:10:39: #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 04:10:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:10:42: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:10:42: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:10:42: #1 total tags in treatment: 15878446 INFO @ Mon, 03 Jun 2019 04:10:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:10:42: #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 04:10:42: #1 tags after filtering in treatment: 15878446 INFO @ Mon, 03 Jun 2019 04:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:10:42: #1 finished! INFO @ Mon, 03 Jun 2019 04:10:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:10:43: 14000000 INFO @ Mon, 03 Jun 2019 04:10:43: #2 number of paired peaks: 113 WARNING @ Mon, 03 Jun 2019 04:10:43: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 03 Jun 2019 04:10:43: start model_add_line... INFO @ Mon, 03 Jun 2019 04:10:43: start X-correlation... INFO @ Mon, 03 Jun 2019 04:10:43: end of X-cor INFO @ Mon, 03 Jun 2019 04:10:43: #2 finished! INFO @ Mon, 03 Jun 2019 04:10:43: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 04:10:43: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 04:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.05_model.r WARNING @ Mon, 03 Jun 2019 04:10:43: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:10:43: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 04:10:43: #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 04:10:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:10:51: 15000000 INFO @ Mon, 03 Jun 2019 04:10:58: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:10:58: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:10:58: #1 total tags in treatment: 15878446 INFO @ Mon, 03 Jun 2019 04:10:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:10:58: #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 04:10:59: #1 tags after filtering in treatment: 15878446 INFO @ Mon, 03 Jun 2019 04:10:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:10:59: #1 finished! INFO @ Mon, 03 Jun 2019 04:10:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:11:00: #2 number of paired peaks: 113 WARNING @ Mon, 03 Jun 2019 04:11:00: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 03 Jun 2019 04:11:00: start model_add_line... INFO @ Mon, 03 Jun 2019 04:11:00: start X-correlation... INFO @ Mon, 03 Jun 2019 04:11:00: end of X-cor INFO @ Mon, 03 Jun 2019 04:11:00: #2 finished! INFO @ Mon, 03 Jun 2019 04:11:00: #2 predicted fragment length is 57 bps INFO @ Mon, 03 Jun 2019 04:11:00: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 03 Jun 2019 04:11:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.20_model.r WARNING @ Mon, 03 Jun 2019 04:11:00: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:11:00: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 03 Jun 2019 04:11:00: #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 04:11:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:11:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:11:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:11:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.10_summits.bed INFO @ Mon, 03 Jun 2019 04:11:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1205 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:11:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:11:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:11:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:11:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.05_summits.bed INFO @ Mon, 03 Jun 2019 04:11:46: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1763 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550619/SRX1550619.20_summits.bed INFO @ Mon, 03 Jun 2019 04:12:03: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (725 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。