Job ID = 4178583 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-05T04:29:10 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 ) 2019-12-05T04:41:44 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 ) 2019-12-05T04:49:17 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 ) 2019-12-05T05:35:33 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 ) 2019-12-05T05:48:51 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 ) 2019-12-05T05:55:41 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 ) 2019-12-05T05:57:13 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 ) 2019-12-05T05:57:42 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 ) 2019-12-05T05:58:54 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 ) 2019-12-05T06:00:10 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 ) 2019-12-05T06:00:54 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 ) 2019-12-05T06:01:25 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 ) 2019-12-05T06:02:12 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 ) 2019-12-05T06:03:45 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 ) 2019-12-05T06:04:24 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 : 87,580,729 reads read : 175,161,458 reads written : 175,161,458 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Multiseed full-index search: 03:11:48 87580729 reads; of these: 87580729 (100.00%) were paired; of these: 50228077 (57.35%) aligned concordantly 0 times 31336662 (35.78%) aligned concordantly exactly 1 time 6015990 (6.87%) aligned concordantly >1 times ---- 50228077 pairs aligned concordantly 0 times; of these: 12132561 (24.15%) aligned discordantly 1 time ---- 38095516 pairs aligned 0 times concordantly or discordantly; of these: 76191032 mates make up the pairs; of these: 69645480 (91.41%) aligned 0 times 2846469 (3.74%) aligned exactly 1 time 3699083 (4.86%) aligned >1 times 60.24% overall alignment rate Time searching: 03:11:49 Overall time: 03:11:49 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 80 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] 46899490 / 48208061 = 0.9729 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 19:12:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.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 @ Thu, 05 Dec 2019 19:12:10: #1 read tag files... INFO @ Thu, 05 Dec 2019 19:12:10: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 19:12:22: 1000000 INFO @ Thu, 05 Dec 2019 19:12:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.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 @ Thu, 05 Dec 2019 19:12:39: #1 read tag files... INFO @ Thu, 05 Dec 2019 19:12:39: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 19:12:48: 2000000 INFO @ Thu, 05 Dec 2019 19:12:57: 1000000 INFO @ Thu, 05 Dec 2019 19:13:03: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 19:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.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 @ Thu, 05 Dec 2019 19:13:08: #1 read tag files... INFO @ Thu, 05 Dec 2019 19:13:08: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 19:13:14: 2000000 INFO @ Thu, 05 Dec 2019 19:13:24: 4000000 INFO @ Thu, 05 Dec 2019 19:13:45: 1000000 INFO @ Thu, 05 Dec 2019 19:13:46: 3000000 INFO @ Thu, 05 Dec 2019 19:14:01: 5000000 INFO @ Thu, 05 Dec 2019 19:14:12: 4000000 INFO @ Thu, 05 Dec 2019 19:14:14: 2000000 INFO @ Thu, 05 Dec 2019 19:14:20: 6000000 INFO @ Thu, 05 Dec 2019 19:14:26: 3000000 INFO @ Thu, 05 Dec 2019 19:14:28: 5000000 INFO @ Thu, 05 Dec 2019 19:14:39: 7000000 INFO @ Thu, 05 Dec 2019 19:14:43: 4000000 INFO @ Thu, 05 Dec 2019 19:14:46: 6000000 INFO @ Thu, 05 Dec 2019 19:14:56: 8000000 INFO @ Thu, 05 Dec 2019 19:14:58: 5000000 INFO @ Thu, 05 Dec 2019 19:15:04: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Dec 2019 19:15:14: 6000000 INFO @ Thu, 05 Dec 2019 19:15:15: 9000000 BigWig に変換しました。 INFO @ Thu, 05 Dec 2019 19:15:22: 8000000 INFO @ Thu, 05 Dec 2019 19:15:32: 7000000 INFO @ Thu, 05 Dec 2019 19:15:35: 10000000 INFO @ Thu, 05 Dec 2019 19:15:42: 9000000 INFO @ Thu, 05 Dec 2019 19:15:48: 8000000 INFO @ Thu, 05 Dec 2019 19:15:55: 11000000 INFO @ Thu, 05 Dec 2019 19:16:02: 10000000 INFO @ Thu, 05 Dec 2019 19:16:06: 9000000 INFO @ Thu, 05 Dec 2019 19:16:09: #1 tag size is determined as 126 bps INFO @ Thu, 05 Dec 2019 19:16:09: #1 tag size = 126 INFO @ Thu, 05 Dec 2019 19:16:09: #1 total tags in treatment: 1842369 INFO @ Thu, 05 Dec 2019 19:16:09: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 19:16:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 19:16:09: #1 tags after filtering in treatment: 708837 INFO @ Thu, 05 Dec 2019 19:16:09: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Dec 2019 19:16:09: #1 finished! INFO @ Thu, 05 Dec 2019 19:16:09: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 19:16:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 19:16:09: #2 number of paired peaks: 4170 INFO @ Thu, 05 Dec 2019 19:16:09: start model_add_line... INFO @ Thu, 05 Dec 2019 19:16:09: start X-correlation... INFO @ Thu, 05 Dec 2019 19:16:09: end of X-cor INFO @ Thu, 05 Dec 2019 19:16:09: #2 finished! INFO @ Thu, 05 Dec 2019 19:16:09: #2 predicted fragment length is 164 bps INFO @ Thu, 05 Dec 2019 19:16:09: #2 alternative fragment length(s) may be 164 bps INFO @ Thu, 05 Dec 2019 19:16:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.05_model.r WARNING @ Thu, 05 Dec 2019 19:16:09: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 19:16:09: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Thu, 05 Dec 2019 19:16:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 19:16:09: #3 Call peaks... INFO @ Thu, 05 Dec 2019 19:16:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 19:16:12: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 19:16:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.05_peaks.xls INFO @ Thu, 05 Dec 2019 19:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 19:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.05_summits.bed INFO @ Thu, 05 Dec 2019 19:16:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2406 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 19:16:20: 11000000 INFO @ Thu, 05 Dec 2019 19:16:24: 10000000 INFO @ Thu, 05 Dec 2019 19:16:31: #1 tag size is determined as 126 bps INFO @ Thu, 05 Dec 2019 19:16:31: #1 tag size = 126 INFO @ Thu, 05 Dec 2019 19:16:31: #1 total tags in treatment: 1842369 INFO @ Thu, 05 Dec 2019 19:16:31: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 19:16:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 19:16:31: #1 tags after filtering in treatment: 708837 INFO @ Thu, 05 Dec 2019 19:16:31: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Dec 2019 19:16:31: #1 finished! INFO @ Thu, 05 Dec 2019 19:16:31: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 19:16:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 19:16:31: #2 number of paired peaks: 4170 INFO @ Thu, 05 Dec 2019 19:16:31: start model_add_line... INFO @ Thu, 05 Dec 2019 19:16:31: start X-correlation... INFO @ Thu, 05 Dec 2019 19:16:31: end of X-cor INFO @ Thu, 05 Dec 2019 19:16:31: #2 finished! INFO @ Thu, 05 Dec 2019 19:16:31: #2 predicted fragment length is 164 bps INFO @ Thu, 05 Dec 2019 19:16:31: #2 alternative fragment length(s) may be 164 bps INFO @ Thu, 05 Dec 2019 19:16:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.10_model.r WARNING @ Thu, 05 Dec 2019 19:16:31: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 19:16:31: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Thu, 05 Dec 2019 19:16:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 19:16:31: #3 Call peaks... INFO @ Thu, 05 Dec 2019 19:16:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 19:16:33: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 19:16:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.10_peaks.xls INFO @ Thu, 05 Dec 2019 19:16:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 19:16:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.10_summits.bed INFO @ Thu, 05 Dec 2019 19:16:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1168 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 19:16:42: 11000000 INFO @ Thu, 05 Dec 2019 19:16:54: #1 tag size is determined as 126 bps INFO @ Thu, 05 Dec 2019 19:16:54: #1 tag size = 126 INFO @ Thu, 05 Dec 2019 19:16:54: #1 total tags in treatment: 1842369 INFO @ Thu, 05 Dec 2019 19:16:54: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 19:16:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 19:16:54: #1 tags after filtering in treatment: 708837 INFO @ Thu, 05 Dec 2019 19:16:54: #1 Redundant rate of treatment: 0.62 INFO @ Thu, 05 Dec 2019 19:16:54: #1 finished! INFO @ Thu, 05 Dec 2019 19:16:54: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 19:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 19:16:54: #2 number of paired peaks: 4170 INFO @ Thu, 05 Dec 2019 19:16:54: start model_add_line... INFO @ Thu, 05 Dec 2019 19:16:54: start X-correlation... INFO @ Thu, 05 Dec 2019 19:16:54: end of X-cor INFO @ Thu, 05 Dec 2019 19:16:54: #2 finished! INFO @ Thu, 05 Dec 2019 19:16:54: #2 predicted fragment length is 164 bps INFO @ Thu, 05 Dec 2019 19:16:54: #2 alternative fragment length(s) may be 164 bps INFO @ Thu, 05 Dec 2019 19:16:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.20_model.r WARNING @ Thu, 05 Dec 2019 19:16:54: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 19:16:54: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Thu, 05 Dec 2019 19:16:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 19:16:54: #3 Call peaks... INFO @ Thu, 05 Dec 2019 19:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 19:16:57: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 19:16:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.20_peaks.xls INFO @ Thu, 05 Dec 2019 19:16:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 19:16:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827847/SRX5827847.20_summits.bed INFO @ Thu, 05 Dec 2019 19:16:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 4 millis CompletedMACS2peakCalling