Job ID = 1293904 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T18:17:22 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 ) 2019-06-02T18:22:03 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 ) 2019-06-02T18:36:33 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T18:42:03 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T19:23:48 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 : 42,264,582 reads read : 84,529,164 reads written : 84,529,164 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: 04:13:27 42264582 reads; of these: 42264582 (100.00%) were paired; of these: 3288355 (7.78%) aligned concordantly 0 times 23554082 (55.73%) aligned concordantly exactly 1 time 15422145 (36.49%) aligned concordantly >1 times ---- 3288355 pairs aligned concordantly 0 times; of these: 511099 (15.54%) aligned discordantly 1 time ---- 2777256 pairs aligned 0 times concordantly or discordantly; of these: 5554512 mates make up the pairs; of these: 3981539 (71.68%) aligned 0 times 670346 (12.07%) aligned exactly 1 time 902627 (16.25%) aligned >1 times 95.29% overall alignment rate Time searching: 04:13:27 Overall time: 04:13:27 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 36 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 21736409 / 39235368 = 0.5540 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 09:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.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 09:15:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:15:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.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 09:15:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:15:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.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 09:15:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:15:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:15:45: 1000000 INFO @ Mon, 03 Jun 2019 09:15:45: 1000000 INFO @ Mon, 03 Jun 2019 09:15:47: 1000000 INFO @ Mon, 03 Jun 2019 09:15:54: 2000000 INFO @ Mon, 03 Jun 2019 09:15:55: 2000000 INFO @ Mon, 03 Jun 2019 09:15:59: 2000000 INFO @ Mon, 03 Jun 2019 09:16:03: 3000000 INFO @ Mon, 03 Jun 2019 09:16:04: 3000000 INFO @ Mon, 03 Jun 2019 09:16:11: 3000000 INFO @ Mon, 03 Jun 2019 09:16:12: 4000000 INFO @ Mon, 03 Jun 2019 09:16:14: 4000000 INFO @ Mon, 03 Jun 2019 09:16:21: 5000000 INFO @ Mon, 03 Jun 2019 09:16:22: 4000000 INFO @ Mon, 03 Jun 2019 09:16:23: 5000000 INFO @ Mon, 03 Jun 2019 09:16:29: 6000000 INFO @ Mon, 03 Jun 2019 09:16:32: 6000000 INFO @ Mon, 03 Jun 2019 09:16:33: 5000000 INFO @ Mon, 03 Jun 2019 09:16:38: 7000000 INFO @ Mon, 03 Jun 2019 09:16:41: 7000000 INFO @ Mon, 03 Jun 2019 09:16:43: 6000000 INFO @ Mon, 03 Jun 2019 09:16:47: 8000000 INFO @ Mon, 03 Jun 2019 09:16:50: 8000000 INFO @ Mon, 03 Jun 2019 09:16:54: 7000000 INFO @ Mon, 03 Jun 2019 09:16:55: 9000000 INFO @ Mon, 03 Jun 2019 09:16:59: 9000000 INFO @ Mon, 03 Jun 2019 09:17:04: 10000000 INFO @ Mon, 03 Jun 2019 09:17:04: 8000000 INFO @ Mon, 03 Jun 2019 09:17:08: 10000000 INFO @ Mon, 03 Jun 2019 09:17:12: 11000000 INFO @ Mon, 03 Jun 2019 09:17:15: 9000000 INFO @ Mon, 03 Jun 2019 09:17:17: 11000000 INFO @ Mon, 03 Jun 2019 09:17:21: 12000000 INFO @ Mon, 03 Jun 2019 09:17:25: 10000000 INFO @ Mon, 03 Jun 2019 09:17:26: 12000000 INFO @ Mon, 03 Jun 2019 09:17:29: 13000000 INFO @ Mon, 03 Jun 2019 09:17:34: 13000000 INFO @ Mon, 03 Jun 2019 09:17:36: 11000000 INFO @ Mon, 03 Jun 2019 09:17:39: 14000000 INFO @ Mon, 03 Jun 2019 09:17:44: 14000000 INFO @ Mon, 03 Jun 2019 09:17:46: 12000000 INFO @ Mon, 03 Jun 2019 09:17:48: 15000000 INFO @ Mon, 03 Jun 2019 09:17:54: 15000000 INFO @ Mon, 03 Jun 2019 09:17:57: 13000000 INFO @ Mon, 03 Jun 2019 09:17:57: 16000000 INFO @ Mon, 03 Jun 2019 09:18:05: 16000000 INFO @ Mon, 03 Jun 2019 09:18:06: 17000000 INFO @ Mon, 03 Jun 2019 09:18:07: 14000000 INFO @ Mon, 03 Jun 2019 09:18:14: 18000000 INFO @ Mon, 03 Jun 2019 09:18:15: 17000000 INFO @ Mon, 03 Jun 2019 09:18:17: 15000000 INFO @ Mon, 03 Jun 2019 09:18:23: 19000000 INFO @ Mon, 03 Jun 2019 09:18:25: 18000000 INFO @ Mon, 03 Jun 2019 09:18:29: 16000000 INFO @ Mon, 03 Jun 2019 09:18:31: 20000000 INFO @ Mon, 03 Jun 2019 09:18:34: 19000000 INFO @ Mon, 03 Jun 2019 09:18:39: 17000000 INFO @ Mon, 03 Jun 2019 09:18:40: 21000000 INFO @ Mon, 03 Jun 2019 09:18:44: 20000000 INFO @ Mon, 03 Jun 2019 09:18:48: 22000000 INFO @ Mon, 03 Jun 2019 09:18:49: 18000000 INFO @ Mon, 03 Jun 2019 09:18:53: 21000000 INFO @ Mon, 03 Jun 2019 09:18:56: 23000000 INFO @ Mon, 03 Jun 2019 09:18:59: 19000000 INFO @ Mon, 03 Jun 2019 09:19:02: 22000000 INFO @ Mon, 03 Jun 2019 09:19:04: 24000000 INFO @ Mon, 03 Jun 2019 09:19:10: 20000000 INFO @ Mon, 03 Jun 2019 09:19:12: 25000000 INFO @ Mon, 03 Jun 2019 09:19:12: 23000000 INFO @ Mon, 03 Jun 2019 09:19:20: 21000000 INFO @ Mon, 03 Jun 2019 09:19:20: 26000000 INFO @ Mon, 03 Jun 2019 09:19:21: 24000000 INFO @ Mon, 03 Jun 2019 09:19:28: 27000000 INFO @ Mon, 03 Jun 2019 09:19:30: 22000000 INFO @ Mon, 03 Jun 2019 09:19:31: 25000000 INFO @ Mon, 03 Jun 2019 09:19:36: 28000000 INFO @ Mon, 03 Jun 2019 09:19:40: 26000000 INFO @ Mon, 03 Jun 2019 09:19:40: 23000000 INFO @ Mon, 03 Jun 2019 09:19:44: 29000000 INFO @ Mon, 03 Jun 2019 09:19:49: 27000000 INFO @ Mon, 03 Jun 2019 09:19:50: 24000000 INFO @ Mon, 03 Jun 2019 09:19:52: 30000000 INFO @ Mon, 03 Jun 2019 09:19:59: 28000000 INFO @ Mon, 03 Jun 2019 09:20:01: 25000000 INFO @ Mon, 03 Jun 2019 09:20:01: 31000000 INFO @ Mon, 03 Jun 2019 09:20:08: 29000000 INFO @ Mon, 03 Jun 2019 09:20:09: 32000000 INFO @ Mon, 03 Jun 2019 09:20:10: 26000000 INFO @ Mon, 03 Jun 2019 09:20:18: 33000000 INFO @ Mon, 03 Jun 2019 09:20:18: 30000000 INFO @ Mon, 03 Jun 2019 09:20:20: 27000000 INFO @ Mon, 03 Jun 2019 09:20:26: 34000000 INFO @ Mon, 03 Jun 2019 09:20:27: 31000000 INFO @ Mon, 03 Jun 2019 09:20:29: 28000000 INFO @ Mon, 03 Jun 2019 09:20:34: 35000000 INFO @ Mon, 03 Jun 2019 09:20:37: 32000000 INFO @ Mon, 03 Jun 2019 09:20:39: 29000000 INFO @ Mon, 03 Jun 2019 09:20:42: 36000000 INFO @ Mon, 03 Jun 2019 09:20:47: 33000000 INFO @ Mon, 03 Jun 2019 09:20:48: 30000000 INFO @ Mon, 03 Jun 2019 09:20:50: 37000000 INFO @ Mon, 03 Jun 2019 09:20:51: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 09:20:51: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 09:20:51: #1 total tags in treatment: 17484787 INFO @ Mon, 03 Jun 2019 09:20:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:20:51: #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 09:20:52: #1 tags after filtering in treatment: 13128343 INFO @ Mon, 03 Jun 2019 09:20:52: #1 Redundant rate of treatment: 0.25 INFO @ Mon, 03 Jun 2019 09:20:52: #1 finished! INFO @ Mon, 03 Jun 2019 09:20:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:20:53: #2 number of paired peaks: 3555 INFO @ Mon, 03 Jun 2019 09:20:53: start model_add_line... INFO @ Mon, 03 Jun 2019 09:20:53: start X-correlation... INFO @ Mon, 03 Jun 2019 09:20:53: end of X-cor INFO @ Mon, 03 Jun 2019 09:20:53: #2 finished! INFO @ Mon, 03 Jun 2019 09:20:53: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 09:20:53: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 09:20:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.10_model.r WARNING @ Mon, 03 Jun 2019 09:20:53: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:20:53: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Mon, 03 Jun 2019 09:20:53: #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 09:20:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:20:57: 34000000 INFO @ Mon, 03 Jun 2019 09:20:58: 31000000 INFO @ Mon, 03 Jun 2019 09:21:06: 35000000 INFO @ Mon, 03 Jun 2019 09:21:08: 32000000 INFO @ Mon, 03 Jun 2019 09:21:16: 36000000 INFO @ Mon, 03 Jun 2019 09:21:17: 33000000 INFO @ Mon, 03 Jun 2019 09:21:25: 37000000 INFO @ Mon, 03 Jun 2019 09:21:26: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 09:21:26: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 09:21:26: #1 total tags in treatment: 17484787 INFO @ Mon, 03 Jun 2019 09:21:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:21:26: #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 09:21:26: #1 tags after filtering in treatment: 13128343 INFO @ Mon, 03 Jun 2019 09:21:26: #1 Redundant rate of treatment: 0.25 INFO @ Mon, 03 Jun 2019 09:21:26: #1 finished! INFO @ Mon, 03 Jun 2019 09:21:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:21:27: 34000000 INFO @ Mon, 03 Jun 2019 09:21:28: #2 number of paired peaks: 3555 INFO @ Mon, 03 Jun 2019 09:21:28: start model_add_line... INFO @ Mon, 03 Jun 2019 09:21:28: start X-correlation... INFO @ Mon, 03 Jun 2019 09:21:28: end of X-cor INFO @ Mon, 03 Jun 2019 09:21:28: #2 finished! INFO @ Mon, 03 Jun 2019 09:21:28: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 09:21:28: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 09:21:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.05_model.r WARNING @ Mon, 03 Jun 2019 09:21:28: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:21:28: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Mon, 03 Jun 2019 09:21:28: #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 09:21:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:21:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:21:36: 35000000 INFO @ Mon, 03 Jun 2019 09:21:45: 36000000 INFO @ Mon, 03 Jun 2019 09:21:54: 37000000 INFO @ Mon, 03 Jun 2019 09:21:55: #1 tag size is determined as 100 bps INFO @ Mon, 03 Jun 2019 09:21:55: #1 tag size = 100 INFO @ Mon, 03 Jun 2019 09:21:55: #1 total tags in treatment: 17484787 INFO @ Mon, 03 Jun 2019 09:21:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:21:55: #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 09:21:56: #1 tags after filtering in treatment: 13128343 INFO @ Mon, 03 Jun 2019 09:21:56: #1 Redundant rate of treatment: 0.25 INFO @ Mon, 03 Jun 2019 09:21:56: #1 finished! INFO @ Mon, 03 Jun 2019 09:21:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.10_summits.bed INFO @ Mon, 03 Jun 2019 09:21:56: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (11630 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:21:57: #2 number of paired peaks: 3555 INFO @ Mon, 03 Jun 2019 09:21:57: start model_add_line... INFO @ Mon, 03 Jun 2019 09:21:57: start X-correlation... INFO @ Mon, 03 Jun 2019 09:21:58: end of X-cor INFO @ Mon, 03 Jun 2019 09:21:58: #2 finished! INFO @ Mon, 03 Jun 2019 09:21:58: #2 predicted fragment length is 158 bps INFO @ Mon, 03 Jun 2019 09:21:58: #2 alternative fragment length(s) may be 158 bps INFO @ Mon, 03 Jun 2019 09:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.20_model.r WARNING @ Mon, 03 Jun 2019 09:21:58: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:21:58: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Mon, 03 Jun 2019 09:21:58: #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 09:21:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:21:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:22:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:22:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:22:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:22:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.05_summits.bed INFO @ Mon, 03 Jun 2019 09:22:32: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (15731 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:22:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:23:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:23:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146999/SRX146999.20_summits.bed INFO @ Mon, 03 Jun 2019 09:23:01: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7690 records, 4 fields): 126 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。