Job ID = 5721229 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T21:02:46 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 ) 2020-04-15T21:02:46 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 ) 2020-04-15T21:02:46 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 ) 2020-04-15T21:02:53 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 ) 2020-04-15T21:02:53 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 ) 2020-04-15T21:04:18 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 ) spots read : 10,424,492 reads read : 20,848,984 reads written : 20,050,936 reads 0-length : 798,048 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] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 2 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 2 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 2 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] processing reference chrUextra... [bam_rmdup_core] 120 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2410609 / 8483182 = 0.2842 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 06:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.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 06:48:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:48:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:48:39: 1000000 INFO @ Thu, 16 Apr 2020 06:48:47: 2000000 INFO @ Thu, 16 Apr 2020 06:48:54: 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 06:49:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.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 06:49:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:49:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:49:02: 4000000 INFO @ Thu, 16 Apr 2020 06:49:08: 1000000 INFO @ Thu, 16 Apr 2020 06:49:10: 5000000 INFO @ Thu, 16 Apr 2020 06:49:16: 2000000 INFO @ Thu, 16 Apr 2020 06:49:18: 6000000 INFO @ Thu, 16 Apr 2020 06:49:23: 3000000 INFO @ Thu, 16 Apr 2020 06:49:26: 7000000 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 06:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.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 06:49:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:49:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:49:31: 4000000 INFO @ Thu, 16 Apr 2020 06:49:34: 8000000 INFO @ Thu, 16 Apr 2020 06:49:40: 1000000 INFO @ Thu, 16 Apr 2020 06:49:41: 5000000 INFO @ Thu, 16 Apr 2020 06:49:44: 9000000 INFO @ Thu, 16 Apr 2020 06:49:50: 2000000 INFO @ Thu, 16 Apr 2020 06:49:51: 6000000 INFO @ Thu, 16 Apr 2020 06:49:53: 10000000 INFO @ Thu, 16 Apr 2020 06:50:00: 7000000 INFO @ Thu, 16 Apr 2020 06:50:00: 3000000 INFO @ Thu, 16 Apr 2020 06:50:02: 11000000 INFO @ Thu, 16 Apr 2020 06:50:09: 8000000 INFO @ Thu, 16 Apr 2020 06:50:09: 4000000 INFO @ Thu, 16 Apr 2020 06:50:12: 12000000 INFO @ Thu, 16 Apr 2020 06:50:18: 9000000 INFO @ Thu, 16 Apr 2020 06:50:18: 5000000 INFO @ Thu, 16 Apr 2020 06:50:21: 13000000 INFO @ Thu, 16 Apr 2020 06:50:22: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:50:22: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:50:22: #1 total tags in treatment: 5946032 INFO @ Thu, 16 Apr 2020 06:50:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:50:22: #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 06:50:23: #1 tags after filtering in treatment: 5617886 INFO @ Thu, 16 Apr 2020 06:50:23: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:50:23: #1 finished! INFO @ Thu, 16 Apr 2020 06:50:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:50:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:50:23: #2 number of paired peaks: 1820 INFO @ Thu, 16 Apr 2020 06:50:23: start model_add_line... INFO @ Thu, 16 Apr 2020 06:50:23: start X-correlation... INFO @ Thu, 16 Apr 2020 06:50:23: end of X-cor INFO @ Thu, 16 Apr 2020 06:50:23: #2 finished! INFO @ Thu, 16 Apr 2020 06:50:23: #2 predicted fragment length is 233 bps INFO @ Thu, 16 Apr 2020 06:50:23: #2 alternative fragment length(s) may be 233 bps INFO @ Thu, 16 Apr 2020 06:50:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.05_model.r WARNING @ Thu, 16 Apr 2020 06:50:23: #2 Since the d (233) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:50:23: #2 You may need to consider one of the other alternative d(s): 233 WARNING @ Thu, 16 Apr 2020 06:50:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:50:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:50:27: 6000000 INFO @ Thu, 16 Apr 2020 06:50:27: 10000000 INFO @ Thu, 16 Apr 2020 06:50:36: 7000000 INFO @ Thu, 16 Apr 2020 06:50:36: 11000000 INFO @ Thu, 16 Apr 2020 06:50:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.05_summits.bed INFO @ Thu, 16 Apr 2020 06:50:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2677 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:50:45: 12000000 INFO @ Thu, 16 Apr 2020 06:50:46: 8000000 INFO @ Thu, 16 Apr 2020 06:50:54: 13000000 INFO @ Thu, 16 Apr 2020 06:50:55: 9000000 INFO @ Thu, 16 Apr 2020 06:50:56: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:50:56: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:50:56: #1 total tags in treatment: 5946032 INFO @ Thu, 16 Apr 2020 06:50:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:50:56: #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 06:50:56: #1 tags after filtering in treatment: 5617886 INFO @ Thu, 16 Apr 2020 06:50:56: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:50:56: #1 finished! INFO @ Thu, 16 Apr 2020 06:50:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:50:56: #2 number of paired peaks: 1820 INFO @ Thu, 16 Apr 2020 06:50:56: start model_add_line... INFO @ Thu, 16 Apr 2020 06:50:56: start X-correlation... INFO @ Thu, 16 Apr 2020 06:50:56: end of X-cor INFO @ Thu, 16 Apr 2020 06:50:56: #2 finished! INFO @ Thu, 16 Apr 2020 06:50:56: #2 predicted fragment length is 233 bps INFO @ Thu, 16 Apr 2020 06:50:56: #2 alternative fragment length(s) may be 233 bps INFO @ Thu, 16 Apr 2020 06:50:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.10_model.r WARNING @ Thu, 16 Apr 2020 06:50:56: #2 Since the d (233) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:50:56: #2 You may need to consider one of the other alternative d(s): 233 WARNING @ Thu, 16 Apr 2020 06:50:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:50:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:50:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:51:03: 10000000 INFO @ Thu, 16 Apr 2020 06:51:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:51:12: 11000000 INFO @ Thu, 16 Apr 2020 06:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.10_summits.bed INFO @ Thu, 16 Apr 2020 06:51:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1569 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:51:21: 12000000 INFO @ Thu, 16 Apr 2020 06:51:29: 13000000 INFO @ Thu, 16 Apr 2020 06:51:31: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:51:31: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:51:31: #1 total tags in treatment: 5946032 INFO @ Thu, 16 Apr 2020 06:51:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:51:31: #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 06:51:31: #1 tags after filtering in treatment: 5617886 INFO @ Thu, 16 Apr 2020 06:51:31: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:51:31: #1 finished! INFO @ Thu, 16 Apr 2020 06:51:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:51:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:51:32: #2 number of paired peaks: 1820 INFO @ Thu, 16 Apr 2020 06:51:32: start model_add_line... INFO @ Thu, 16 Apr 2020 06:51:32: start X-correlation... INFO @ Thu, 16 Apr 2020 06:51:32: end of X-cor INFO @ Thu, 16 Apr 2020 06:51:32: #2 finished! INFO @ Thu, 16 Apr 2020 06:51:32: #2 predicted fragment length is 233 bps INFO @ Thu, 16 Apr 2020 06:51:32: #2 alternative fragment length(s) may be 233 bps INFO @ Thu, 16 Apr 2020 06:51:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.20_model.r WARNING @ Thu, 16 Apr 2020 06:51:32: #2 Since the d (233) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:51:32: #2 You may need to consider one of the other alternative d(s): 233 WARNING @ Thu, 16 Apr 2020 06:51:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:51:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:51:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:51:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:51:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:51:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:51:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050416/SRX7050416.20_summits.bed INFO @ Thu, 16 Apr 2020 06:51:52: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (852 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。