Job ID = 5790788 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T22:15:32 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 : 4,373,395 reads read : 8,746,790 reads written : 4,373,395 reads 0-length : 4,373,395 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:33 4373395 reads; of these: 4373395 (100.00%) were unpaired; of these: 442345 (10.11%) aligned 0 times 2827640 (64.66%) aligned exactly 1 time 1103410 (25.23%) aligned >1 times 89.89% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 295850 / 3931050 = 0.0753 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 @ Wed, 22 Apr 2020 07:22:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 07:22:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:22:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:22:28: 1000000 INFO @ Wed, 22 Apr 2020 07:22:34: 2000000 INFO @ Wed, 22 Apr 2020 07:22:41: 3000000 INFO @ Wed, 22 Apr 2020 07:22:45: #1 tag size is determined as 73 bps INFO @ Wed, 22 Apr 2020 07:22:45: #1 tag size = 73 INFO @ Wed, 22 Apr 2020 07:22:45: #1 total tags in treatment: 3635200 INFO @ Wed, 22 Apr 2020 07:22:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:22:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:22:45: #1 tags after filtering in treatment: 3634908 INFO @ Wed, 22 Apr 2020 07:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:22:45: #1 finished! INFO @ Wed, 22 Apr 2020 07:22:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:22:47: #2 number of paired peaks: 6929 INFO @ Wed, 22 Apr 2020 07:22:47: start model_add_line... INFO @ Wed, 22 Apr 2020 07:22:47: start X-correlation... INFO @ Wed, 22 Apr 2020 07:22:47: end of X-cor INFO @ Wed, 22 Apr 2020 07:22:47: #2 finished! INFO @ Wed, 22 Apr 2020 07:22:47: #2 predicted fragment length is 79 bps INFO @ Wed, 22 Apr 2020 07:22:47: #2 alternative fragment length(s) may be 79,127,151,188,259 bps INFO @ Wed, 22 Apr 2020 07:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.05_model.r WARNING @ Wed, 22 Apr 2020 07:22:47: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:22:47: #2 You may need to consider one of the other alternative d(s): 79,127,151,188,259 WARNING @ Wed, 22 Apr 2020 07:22:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:22:47: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:22:47: #3 Pre-compute pvalue-qvalue table... 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 @ Wed, 22 Apr 2020 07:22:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 07:22:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:22:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:22:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:22:57: 1000000 INFO @ Wed, 22 Apr 2020 07:22:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:22:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:22:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.05_summits.bed INFO @ Wed, 22 Apr 2020 07:22:59: Done! pass1 - making usageList (45 chroms): 0 millis pass2 - checking and writing primary data (442 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:23:04: 2000000 INFO @ Wed, 22 Apr 2020 07:23:11: 3000000 INFO @ Wed, 22 Apr 2020 07:23:15: #1 tag size is determined as 73 bps INFO @ Wed, 22 Apr 2020 07:23:15: #1 tag size = 73 INFO @ Wed, 22 Apr 2020 07:23:15: #1 total tags in treatment: 3635200 INFO @ Wed, 22 Apr 2020 07:23:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:23:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:23:15: #1 tags after filtering in treatment: 3634908 INFO @ Wed, 22 Apr 2020 07:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:23:15: #1 finished! INFO @ Wed, 22 Apr 2020 07:23:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:23:17: #2 number of paired peaks: 6929 INFO @ Wed, 22 Apr 2020 07:23:17: start model_add_line... INFO @ Wed, 22 Apr 2020 07:23:17: start X-correlation... INFO @ Wed, 22 Apr 2020 07:23:17: end of X-cor INFO @ Wed, 22 Apr 2020 07:23:17: #2 finished! INFO @ Wed, 22 Apr 2020 07:23:17: #2 predicted fragment length is 79 bps INFO @ Wed, 22 Apr 2020 07:23:17: #2 alternative fragment length(s) may be 79,127,151,188,259 bps INFO @ Wed, 22 Apr 2020 07:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.10_model.r WARNING @ Wed, 22 Apr 2020 07:23:17: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:23:17: #2 You may need to consider one of the other alternative d(s): 79,127,151,188,259 WARNING @ Wed, 22 Apr 2020 07:23:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:23:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:23:17: #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 @ Wed, 22 Apr 2020 07:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 07:23:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:23:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:23:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:23:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:23:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:23:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.10_summits.bed INFO @ Wed, 22 Apr 2020 07:23:29: Done! INFO @ Wed, 22 Apr 2020 07:23:29: 1000000 pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:23:38: 2000000 INFO @ Wed, 22 Apr 2020 07:23:46: 3000000 INFO @ Wed, 22 Apr 2020 07:23:51: #1 tag size is determined as 73 bps INFO @ Wed, 22 Apr 2020 07:23:51: #1 tag size = 73 INFO @ Wed, 22 Apr 2020 07:23:51: #1 total tags in treatment: 3635200 INFO @ Wed, 22 Apr 2020 07:23:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:23:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:23:51: #1 tags after filtering in treatment: 3634908 INFO @ Wed, 22 Apr 2020 07:23:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:23:51: #1 finished! INFO @ Wed, 22 Apr 2020 07:23:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:23:53: #2 number of paired peaks: 6929 INFO @ Wed, 22 Apr 2020 07:23:53: start model_add_line... INFO @ Wed, 22 Apr 2020 07:23:53: start X-correlation... INFO @ Wed, 22 Apr 2020 07:23:53: end of X-cor INFO @ Wed, 22 Apr 2020 07:23:53: #2 finished! INFO @ Wed, 22 Apr 2020 07:23:53: #2 predicted fragment length is 79 bps INFO @ Wed, 22 Apr 2020 07:23:53: #2 alternative fragment length(s) may be 79,127,151,188,259 bps INFO @ Wed, 22 Apr 2020 07:23:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.20_model.r WARNING @ Wed, 22 Apr 2020 07:23:53: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:23:53: #2 You may need to consider one of the other alternative d(s): 79,127,151,188,259 WARNING @ Wed, 22 Apr 2020 07:23:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:23:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:24:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:24:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:24:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:24:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625158/SRX7625158.20_summits.bed INFO @ Wed, 22 Apr 2020 07:24:05: Done! pass1 - making usageList (26 chroms): 0 millis pass2 - checking and writing primary data (145 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。