Job ID = 5721257 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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 ) 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 : 8,261,462 reads read : 16,522,924 reads written : 15,580,870 reads 0-length : 942,054 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] 1 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] 2 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 5 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] 157 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1129809 / 6943223 = 0.1627 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 06:49:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.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 06:49:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:49:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:50:00: 1000000 INFO @ Thu, 16 Apr 2020 06:50:07: 2000000 INFO @ Thu, 16 Apr 2020 06:50:14: 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 06:50:21: 4000000 INFO @ Thu, 16 Apr 2020 06:50:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.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 06:50:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:50:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:50:29: 5000000 INFO @ Thu, 16 Apr 2020 06:50:31: 1000000 INFO @ Thu, 16 Apr 2020 06:50:38: 6000000 INFO @ Thu, 16 Apr 2020 06:50:39: 2000000 INFO @ Thu, 16 Apr 2020 06:50:46: 7000000 INFO @ Thu, 16 Apr 2020 06:50:48: 3000000 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 06:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.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 06:50:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:50:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:50:55: 8000000 INFO @ Thu, 16 Apr 2020 06:50:56: 4000000 INFO @ Thu, 16 Apr 2020 06:51:01: 1000000 INFO @ Thu, 16 Apr 2020 06:51:03: 9000000 INFO @ Thu, 16 Apr 2020 06:51:05: 5000000 INFO @ Thu, 16 Apr 2020 06:51:10: 2000000 INFO @ Thu, 16 Apr 2020 06:51:12: 10000000 INFO @ Thu, 16 Apr 2020 06:51:13: 6000000 INFO @ Thu, 16 Apr 2020 06:51:18: 3000000 INFO @ Thu, 16 Apr 2020 06:51:20: 11000000 INFO @ Thu, 16 Apr 2020 06:51:22: 7000000 INFO @ Thu, 16 Apr 2020 06:51:27: 4000000 INFO @ Thu, 16 Apr 2020 06:51:29: 12000000 INFO @ Thu, 16 Apr 2020 06:51:30: 8000000 INFO @ Thu, 16 Apr 2020 06:51:35: 5000000 INFO @ Thu, 16 Apr 2020 06:51:36: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:51:36: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:51:36: #1 total tags in treatment: 5698417 INFO @ Thu, 16 Apr 2020 06:51:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:51:36: #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 06:51:36: #1 tags after filtering in treatment: 5369033 INFO @ Thu, 16 Apr 2020 06:51:36: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:51:36: #1 finished! INFO @ Thu, 16 Apr 2020 06:51:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:51:37: #2 number of paired peaks: 1613 INFO @ Thu, 16 Apr 2020 06:51:37: start model_add_line... INFO @ Thu, 16 Apr 2020 06:51:37: start X-correlation... INFO @ Thu, 16 Apr 2020 06:51:37: end of X-cor INFO @ Thu, 16 Apr 2020 06:51:37: #2 finished! INFO @ Thu, 16 Apr 2020 06:51:37: #2 predicted fragment length is 223 bps INFO @ Thu, 16 Apr 2020 06:51:37: #2 alternative fragment length(s) may be 223 bps INFO @ Thu, 16 Apr 2020 06:51:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.05_model.r WARNING @ Thu, 16 Apr 2020 06:51:37: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:51:37: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Thu, 16 Apr 2020 06:51:37: #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 06:51:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:51:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:51:39: 9000000 INFO @ Thu, 16 Apr 2020 06:51:44: 6000000 INFO @ Thu, 16 Apr 2020 06:51:47: 10000000 INFO @ Thu, 16 Apr 2020 06:51:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:51:52: 7000000 INFO @ Thu, 16 Apr 2020 06:51:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:51:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:51:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.05_summits.bed INFO @ Thu, 16 Apr 2020 06:51:56: Done! INFO @ Thu, 16 Apr 2020 06:51:56: 11000000 pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1822 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:52:01: 8000000 INFO @ Thu, 16 Apr 2020 06:52:05: 12000000 INFO @ Thu, 16 Apr 2020 06:52:09: 9000000 INFO @ Thu, 16 Apr 2020 06:52:12: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:52:12: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:52:12: #1 total tags in treatment: 5698417 INFO @ Thu, 16 Apr 2020 06:52:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:52:12: #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 06:52:12: #1 tags after filtering in treatment: 5369033 INFO @ Thu, 16 Apr 2020 06:52:12: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:52:12: #1 finished! INFO @ Thu, 16 Apr 2020 06:52:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:52:12: #2 number of paired peaks: 1613 INFO @ Thu, 16 Apr 2020 06:52:12: start model_add_line... INFO @ Thu, 16 Apr 2020 06:52:12: start X-correlation... INFO @ Thu, 16 Apr 2020 06:52:12: end of X-cor INFO @ Thu, 16 Apr 2020 06:52:12: #2 finished! INFO @ Thu, 16 Apr 2020 06:52:12: #2 predicted fragment length is 223 bps INFO @ Thu, 16 Apr 2020 06:52:12: #2 alternative fragment length(s) may be 223 bps INFO @ Thu, 16 Apr 2020 06:52:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.10_model.r WARNING @ Thu, 16 Apr 2020 06:52:12: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:52:12: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Thu, 16 Apr 2020 06:52:12: #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 06:52:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:52:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:52:17: 10000000 INFO @ Thu, 16 Apr 2020 06:52:25: 11000000 INFO @ Thu, 16 Apr 2020 06:52:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.10_summits.bed INFO @ Thu, 16 Apr 2020 06:52:31: Done! INFO @ Thu, 16 Apr 2020 06:52:33: 12000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1209 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:52:39: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:52:39: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:52:39: #1 total tags in treatment: 5698417 INFO @ Thu, 16 Apr 2020 06:52:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:52:39: #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 06:52:39: #1 tags after filtering in treatment: 5369033 INFO @ Thu, 16 Apr 2020 06:52:39: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 06:52:39: #1 finished! INFO @ Thu, 16 Apr 2020 06:52:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:52:40: #2 number of paired peaks: 1613 INFO @ Thu, 16 Apr 2020 06:52:40: start model_add_line... INFO @ Thu, 16 Apr 2020 06:52:40: start X-correlation... INFO @ Thu, 16 Apr 2020 06:52:40: end of X-cor INFO @ Thu, 16 Apr 2020 06:52:40: #2 finished! INFO @ Thu, 16 Apr 2020 06:52:40: #2 predicted fragment length is 223 bps INFO @ Thu, 16 Apr 2020 06:52:40: #2 alternative fragment length(s) may be 223 bps INFO @ Thu, 16 Apr 2020 06:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.20_model.r WARNING @ Thu, 16 Apr 2020 06:52:40: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:52:40: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Thu, 16 Apr 2020 06:52:40: #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 06:52:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:52:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:52:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:52:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050430/SRX7050430.20_summits.bed INFO @ Thu, 16 Apr 2020 06:52:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (739 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。