Job ID = 5721244 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T21:05:13 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 ) 2020-04-15T21:09:17 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 ) spots read : 6,299,563 reads read : 12,599,126 reads written : 11,881,010 reads 0-length : 718,116 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 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 3 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 5 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 3 unmatched pairs [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] 18 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] 883298 / 5216431 = 0.1693 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 06:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.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 06:39:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:39:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:39:45: 1000000 INFO @ Thu, 16 Apr 2020 06:39:51: 2000000 INFO @ Thu, 16 Apr 2020 06:39:56: 3000000 INFO @ Thu, 16 Apr 2020 06:40:02: 4000000 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 06:40:08: 5000000 INFO @ Thu, 16 Apr 2020 06:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.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 06:40:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:40:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:40:14: 6000000 INFO @ Thu, 16 Apr 2020 06:40:15: 1000000 INFO @ Thu, 16 Apr 2020 06:40:20: 7000000 INFO @ Thu, 16 Apr 2020 06:40:21: 2000000 INFO @ Thu, 16 Apr 2020 06:40:26: 8000000 INFO @ Thu, 16 Apr 2020 06:40:27: 3000000 INFO @ Thu, 16 Apr 2020 06:40:32: 9000000 INFO @ Thu, 16 Apr 2020 06:40:33: 4000000 INFO @ Thu, 16 Apr 2020 06:40:35: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:40:35: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:40:35: #1 total tags in treatment: 4171979 INFO @ Thu, 16 Apr 2020 06:40:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:40:35: #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 06:40:35: #1 tags after filtering in treatment: 3884227 INFO @ Thu, 16 Apr 2020 06:40:35: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:40:35: #1 finished! INFO @ Thu, 16 Apr 2020 06:40:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:40:36: #2 number of paired peaks: 4330 INFO @ Thu, 16 Apr 2020 06:40:36: start model_add_line... INFO @ Thu, 16 Apr 2020 06:40:36: start X-correlation... INFO @ Thu, 16 Apr 2020 06:40:36: end of X-cor INFO @ Thu, 16 Apr 2020 06:40:36: #2 finished! INFO @ Thu, 16 Apr 2020 06:40:36: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 06:40:36: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 06:40:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.05_model.r WARNING @ Thu, 16 Apr 2020 06:40:36: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:40:36: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Thu, 16 Apr 2020 06:40:36: #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 06:40:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:40:36: #3 Pre-compute pvalue-qvalue table... 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 06:40:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.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 06:40:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:40:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:40:39: 5000000 INFO @ Thu, 16 Apr 2020 06:40:45: 1000000 INFO @ Thu, 16 Apr 2020 06:40:45: 6000000 INFO @ Thu, 16 Apr 2020 06:40:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.05_summits.bed INFO @ Thu, 16 Apr 2020 06:40:51: Done! INFO @ Thu, 16 Apr 2020 06:40:51: 2000000 INFO @ Thu, 16 Apr 2020 06:40:52: 7000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6333 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:40:57: 3000000 INFO @ Thu, 16 Apr 2020 06:40:58: 8000000 INFO @ Thu, 16 Apr 2020 06:41:03: 4000000 INFO @ Thu, 16 Apr 2020 06:41:04: 9000000 INFO @ Thu, 16 Apr 2020 06:41:07: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:41:07: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:41:07: #1 total tags in treatment: 4171979 INFO @ Thu, 16 Apr 2020 06:41:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:41:07: #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 06:41:07: #1 tags after filtering in treatment: 3884227 INFO @ Thu, 16 Apr 2020 06:41:07: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:41:07: #1 finished! INFO @ Thu, 16 Apr 2020 06:41:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:41:08: #2 number of paired peaks: 4330 INFO @ Thu, 16 Apr 2020 06:41:08: start model_add_line... INFO @ Thu, 16 Apr 2020 06:41:08: start X-correlation... INFO @ Thu, 16 Apr 2020 06:41:08: end of X-cor INFO @ Thu, 16 Apr 2020 06:41:08: #2 finished! INFO @ Thu, 16 Apr 2020 06:41:08: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 06:41:08: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 06:41:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.10_model.r WARNING @ Thu, 16 Apr 2020 06:41:08: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:41:08: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Thu, 16 Apr 2020 06:41:08: #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 06:41:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:41:09: 5000000 INFO @ Thu, 16 Apr 2020 06:41:15: 6000000 INFO @ Thu, 16 Apr 2020 06:41:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:41:21: 7000000 INFO @ Thu, 16 Apr 2020 06:41:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:41:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:41:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.10_summits.bed INFO @ Thu, 16 Apr 2020 06:41:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4027 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:41:27: 8000000 INFO @ Thu, 16 Apr 2020 06:41:33: 9000000 INFO @ Thu, 16 Apr 2020 06:41:37: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:41:37: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:41:37: #1 total tags in treatment: 4171979 INFO @ Thu, 16 Apr 2020 06:41:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:41:37: #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 06:41:37: #1 tags after filtering in treatment: 3884227 INFO @ Thu, 16 Apr 2020 06:41:37: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 16 Apr 2020 06:41:37: #1 finished! INFO @ Thu, 16 Apr 2020 06:41:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:41:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:41:37: #2 number of paired peaks: 4330 INFO @ Thu, 16 Apr 2020 06:41:37: start model_add_line... INFO @ Thu, 16 Apr 2020 06:41:37: start X-correlation... INFO @ Thu, 16 Apr 2020 06:41:37: end of X-cor INFO @ Thu, 16 Apr 2020 06:41:37: #2 finished! INFO @ Thu, 16 Apr 2020 06:41:37: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 06:41:37: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 06:41:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.20_model.r WARNING @ Thu, 16 Apr 2020 06:41:37: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:41:37: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Thu, 16 Apr 2020 06:41:37: #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 06:41:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:41:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:41:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:41:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:41:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:41:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050424/SRX7050424.20_summits.bed INFO @ Thu, 16 Apr 2020 06:41:52: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2354 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。