Job ID = 5720770 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:17:24 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 ) 2020-04-15T16:17:24 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 ) 2020-04-15T16:17:24 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 : 1,350,294 reads read : 2,700,588 reads written : 2,700,588 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 Multiseed full-index search: 00:07:16 1350294 reads; of these: 1350294 (100.00%) were paired; of these: 172332 (12.76%) aligned concordantly 0 times 379999 (28.14%) aligned concordantly exactly 1 time 797963 (59.10%) aligned concordantly >1 times ---- 172332 pairs aligned concordantly 0 times; of these: 29013 (16.84%) aligned discordantly 1 time ---- 143319 pairs aligned 0 times concordantly or discordantly; of these: 286638 mates make up the pairs; of these: 136065 (47.47%) aligned 0 times 71085 (24.80%) aligned exactly 1 time 79488 (27.73%) aligned >1 times 94.96% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 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_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] 139635 / 1186001 = 0.1177 in library ' ' 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 01:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.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 01:26:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:26:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:26:46: 1000000 INFO @ Thu, 16 Apr 2020 01:26:51: 2000000 INFO @ Thu, 16 Apr 2020 01:26:53: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 01:26:53: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 01:26:53: #1 total tags in treatment: 1039123 INFO @ Thu, 16 Apr 2020 01:26:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:26:53: #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 01:26:53: #1 tags after filtering in treatment: 869011 INFO @ Thu, 16 Apr 2020 01:26:53: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 01:26:53: #1 finished! INFO @ Thu, 16 Apr 2020 01:26:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:26:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:26:53: #2 number of paired peaks: 3348 INFO @ Thu, 16 Apr 2020 01:26:53: start model_add_line... INFO @ Thu, 16 Apr 2020 01:26:53: start X-correlation... INFO @ Thu, 16 Apr 2020 01:26:53: end of X-cor INFO @ Thu, 16 Apr 2020 01:26:53: #2 finished! INFO @ Thu, 16 Apr 2020 01:26:53: #2 predicted fragment length is 136 bps INFO @ Thu, 16 Apr 2020 01:26:53: #2 alternative fragment length(s) may be 136 bps INFO @ Thu, 16 Apr 2020 01:26:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.05_model.r WARNING @ Thu, 16 Apr 2020 01:26:53: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:26:53: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Thu, 16 Apr 2020 01:26:53: #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 01:26:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:26:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:26:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:26:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:26:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:26:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.05_summits.bed INFO @ Thu, 16 Apr 2020 01:26:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2139 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 01:27:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.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 01:27:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:27:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:27:16: 1000000 INFO @ Thu, 16 Apr 2020 01:27:21: 2000000 INFO @ Thu, 16 Apr 2020 01:27:23: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 01:27:23: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 01:27:23: #1 total tags in treatment: 1039123 INFO @ Thu, 16 Apr 2020 01:27:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:27:23: #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 01:27:23: #1 tags after filtering in treatment: 869011 INFO @ Thu, 16 Apr 2020 01:27:23: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 01:27:23: #1 finished! INFO @ Thu, 16 Apr 2020 01:27:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:27:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:27:23: #2 number of paired peaks: 3348 INFO @ Thu, 16 Apr 2020 01:27:23: start model_add_line... INFO @ Thu, 16 Apr 2020 01:27:23: start X-correlation... INFO @ Thu, 16 Apr 2020 01:27:23: end of X-cor INFO @ Thu, 16 Apr 2020 01:27:23: #2 finished! INFO @ Thu, 16 Apr 2020 01:27:23: #2 predicted fragment length is 136 bps INFO @ Thu, 16 Apr 2020 01:27:23: #2 alternative fragment length(s) may be 136 bps INFO @ Thu, 16 Apr 2020 01:27:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.10_model.r WARNING @ Thu, 16 Apr 2020 01:27:23: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:27:23: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Thu, 16 Apr 2020 01:27:23: #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 01:27:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:27:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:27:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.10_summits.bed INFO @ Thu, 16 Apr 2020 01:27:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1404 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 01:27:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.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 01:27:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:27:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:27:47: 1000000 INFO @ Thu, 16 Apr 2020 01:27:53: 2000000 INFO @ Thu, 16 Apr 2020 01:27:55: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 01:27:55: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 01:27:55: #1 total tags in treatment: 1039123 INFO @ Thu, 16 Apr 2020 01:27:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:27:55: #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 01:27:55: #1 tags after filtering in treatment: 869011 INFO @ Thu, 16 Apr 2020 01:27:55: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 01:27:55: #1 finished! INFO @ Thu, 16 Apr 2020 01:27:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:27:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:27:55: #2 number of paired peaks: 3348 INFO @ Thu, 16 Apr 2020 01:27:55: start model_add_line... INFO @ Thu, 16 Apr 2020 01:27:55: start X-correlation... INFO @ Thu, 16 Apr 2020 01:27:55: end of X-cor INFO @ Thu, 16 Apr 2020 01:27:55: #2 finished! INFO @ Thu, 16 Apr 2020 01:27:55: #2 predicted fragment length is 136 bps INFO @ Thu, 16 Apr 2020 01:27:55: #2 alternative fragment length(s) may be 136 bps INFO @ Thu, 16 Apr 2020 01:27:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.20_model.r WARNING @ Thu, 16 Apr 2020 01:27:55: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:27:55: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Thu, 16 Apr 2020 01:27:55: #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 01:27:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:27:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:27:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:27:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:27:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:27:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227007/SRX5227007.20_summits.bed INFO @ Thu, 16 Apr 2020 01:27:58: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (894 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。