Job ID = 5721253 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T21:04:52 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 ) 2020-04-15T21:04:52 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 ) 2020-04-15T21:04:52 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 ) 2020-04-15T21:04:52 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 ) 2020-04-15T21:09:28 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 ) 2020-04-15T21:13:25 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 ) spots read : 8,913,912 reads read : 17,827,824 reads written : 16,437,309 reads 0-length : 1,390,515 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: 00:00:00 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 5 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 6 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 4 unmatched pairs [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] 1 unmatched pairs [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] 146 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1771751 / 6876923 = 0.2576 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:46:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.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, 16 Apr 2020 06:46:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:46:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:46:32: 1000000 INFO @ Thu, 16 Apr 2020 06:46:41: 2000000 INFO @ Thu, 16 Apr 2020 06:46:50: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:46:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.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, 16 Apr 2020 06:46:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:46:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:46:58: 4000000 INFO @ Thu, 16 Apr 2020 06:47:05: 1000000 INFO @ Thu, 16 Apr 2020 06:47:08: 5000000 INFO @ Thu, 16 Apr 2020 06:47:15: 2000000 INFO @ Thu, 16 Apr 2020 06:47:18: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.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, 16 Apr 2020 06:47:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:47:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:47:26: 3000000 INFO @ Thu, 16 Apr 2020 06:47:28: 7000000 INFO @ Thu, 16 Apr 2020 06:47:34: 1000000 INFO @ Thu, 16 Apr 2020 06:47:36: 4000000 INFO @ Thu, 16 Apr 2020 06:47:37: 8000000 INFO @ Thu, 16 Apr 2020 06:47:44: 2000000 INFO @ Thu, 16 Apr 2020 06:47:47: 5000000 INFO @ Thu, 16 Apr 2020 06:47:47: 9000000 INFO @ Thu, 16 Apr 2020 06:47:54: 3000000 INFO @ Thu, 16 Apr 2020 06:47:57: 10000000 INFO @ Thu, 16 Apr 2020 06:47:57: 6000000 INFO @ Thu, 16 Apr 2020 06:48:04: 4000000 INFO @ Thu, 16 Apr 2020 06:48:07: 11000000 INFO @ Thu, 16 Apr 2020 06:48:08: 7000000 INFO @ Thu, 16 Apr 2020 06:48:14: 5000000 INFO @ Thu, 16 Apr 2020 06:48:14: #1 tag size is determined as 123 bps INFO @ Thu, 16 Apr 2020 06:48:14: #1 tag size = 123 INFO @ Thu, 16 Apr 2020 06:48:14: #1 total tags in treatment: 4971216 INFO @ Thu, 16 Apr 2020 06:48:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:48:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:48:15: #1 tags after filtering in treatment: 4198060 INFO @ Thu, 16 Apr 2020 06:48:15: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 06:48:15: #1 finished! INFO @ Thu, 16 Apr 2020 06:48:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:48:15: #2 number of paired peaks: 4885 INFO @ Thu, 16 Apr 2020 06:48:15: start model_add_line... INFO @ Thu, 16 Apr 2020 06:48:15: start X-correlation... INFO @ Thu, 16 Apr 2020 06:48:15: end of X-cor INFO @ Thu, 16 Apr 2020 06:48:15: #2 finished! INFO @ Thu, 16 Apr 2020 06:48:15: #2 predicted fragment length is 267 bps INFO @ Thu, 16 Apr 2020 06:48:15: #2 alternative fragment length(s) may be 267 bps INFO @ Thu, 16 Apr 2020 06:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.05_model.r INFO @ Thu, 16 Apr 2020 06:48:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:48:18: 8000000 INFO @ Thu, 16 Apr 2020 06:48:23: 6000000 INFO @ Thu, 16 Apr 2020 06:48:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:48:29: 9000000 INFO @ Thu, 16 Apr 2020 06:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.05_summits.bed INFO @ Thu, 16 Apr 2020 06:48:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6356 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:48:33: 7000000 INFO @ Thu, 16 Apr 2020 06:48:39: 10000000 INFO @ Thu, 16 Apr 2020 06:48:43: 8000000 INFO @ Thu, 16 Apr 2020 06:48:50: 11000000 INFO @ Thu, 16 Apr 2020 06:48:53: 9000000 INFO @ Thu, 16 Apr 2020 06:48:58: #1 tag size is determined as 123 bps INFO @ Thu, 16 Apr 2020 06:48:58: #1 tag size = 123 INFO @ Thu, 16 Apr 2020 06:48:58: #1 total tags in treatment: 4971216 INFO @ Thu, 16 Apr 2020 06:48:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:48:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:48:58: #1 tags after filtering in treatment: 4198060 INFO @ Thu, 16 Apr 2020 06:48:58: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 06:48:58: #1 finished! INFO @ Thu, 16 Apr 2020 06:48:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:48:59: #2 number of paired peaks: 4885 INFO @ Thu, 16 Apr 2020 06:48:59: start model_add_line... INFO @ Thu, 16 Apr 2020 06:48:59: start X-correlation... INFO @ Thu, 16 Apr 2020 06:48:59: end of X-cor INFO @ Thu, 16 Apr 2020 06:48:59: #2 finished! INFO @ Thu, 16 Apr 2020 06:48:59: #2 predicted fragment length is 267 bps INFO @ Thu, 16 Apr 2020 06:48:59: #2 alternative fragment length(s) may be 267 bps INFO @ Thu, 16 Apr 2020 06:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.10_model.r INFO @ Thu, 16 Apr 2020 06:48:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:49:03: 10000000 INFO @ Thu, 16 Apr 2020 06:49:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:49:12: 11000000 INFO @ Thu, 16 Apr 2020 06:49:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:49:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:49:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.10_summits.bed INFO @ Thu, 16 Apr 2020 06:49:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4885 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:49:19: #1 tag size is determined as 123 bps INFO @ Thu, 16 Apr 2020 06:49:19: #1 tag size = 123 INFO @ Thu, 16 Apr 2020 06:49:19: #1 total tags in treatment: 4971216 INFO @ Thu, 16 Apr 2020 06:49:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:49:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:49:19: #1 tags after filtering in treatment: 4198060 INFO @ Thu, 16 Apr 2020 06:49:19: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 06:49:19: #1 finished! INFO @ Thu, 16 Apr 2020 06:49:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:49:19: #2 number of paired peaks: 4885 INFO @ Thu, 16 Apr 2020 06:49:19: start model_add_line... INFO @ Thu, 16 Apr 2020 06:49:19: start X-correlation... INFO @ Thu, 16 Apr 2020 06:49:19: end of X-cor INFO @ Thu, 16 Apr 2020 06:49:19: #2 finished! INFO @ Thu, 16 Apr 2020 06:49:19: #2 predicted fragment length is 267 bps INFO @ Thu, 16 Apr 2020 06:49:19: #2 alternative fragment length(s) may be 267 bps INFO @ Thu, 16 Apr 2020 06:49:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.20_model.r INFO @ Thu, 16 Apr 2020 06:49:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:49:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 06:49:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:49:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:49:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:49:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050427/SRX7050427.20_summits.bed INFO @ Thu, 16 Apr 2020 06:49:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3462 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。