Job ID = 5720738 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:06:33 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 ) 2020-04-15T16:06:33 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 : 9,889,887 reads read : 19,779,774 reads written : 9,889,887 reads 0-length : 9,889,887 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: 00:06:16 9889887 reads; of these: 9889887 (100.00%) were unpaired; of these: 1197926 (12.11%) aligned 0 times 4759395 (48.12%) aligned exactly 1 time 3932566 (39.76%) aligned >1 times 87.89% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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_rmdupse_core] 1753003 / 8691961 = 0.2017 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 01:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.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 01:19:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:19:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:19:49: 1000000 INFO @ Thu, 16 Apr 2020 01:19:56: 2000000 INFO @ Thu, 16 Apr 2020 01:20:02: 3000000 INFO @ Thu, 16 Apr 2020 01:20:08: 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 01:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.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 01:20:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:20:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:20:15: 5000000 INFO @ Thu, 16 Apr 2020 01:20:21: 1000000 INFO @ Thu, 16 Apr 2020 01:20:22: 6000000 INFO @ Thu, 16 Apr 2020 01:20:30: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:20:30: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:20:30: #1 total tags in treatment: 6938958 INFO @ Thu, 16 Apr 2020 01:20:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:20:30: #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 01:20:30: #1 tags after filtering in treatment: 6938958 INFO @ Thu, 16 Apr 2020 01:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:20:30: #1 finished! INFO @ Thu, 16 Apr 2020 01:20:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:20:30: 2000000 INFO @ Thu, 16 Apr 2020 01:20:30: #2 number of paired peaks: 2085 INFO @ Thu, 16 Apr 2020 01:20:30: start model_add_line... INFO @ Thu, 16 Apr 2020 01:20:30: start X-correlation... INFO @ Thu, 16 Apr 2020 01:20:30: end of X-cor INFO @ Thu, 16 Apr 2020 01:20:30: #2 finished! INFO @ Thu, 16 Apr 2020 01:20:30: #2 predicted fragment length is 98 bps INFO @ Thu, 16 Apr 2020 01:20:30: #2 alternative fragment length(s) may be 98 bps INFO @ Thu, 16 Apr 2020 01:20:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.05_model.r WARNING @ Thu, 16 Apr 2020 01:20:30: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:20:30: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Thu, 16 Apr 2020 01:20:30: #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 01:20:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:20:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:20:38: 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 01:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.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 01:20:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:20:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:20:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:20:46: 4000000 INFO @ Thu, 16 Apr 2020 01:20:51: 1000000 INFO @ Thu, 16 Apr 2020 01:20:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:20:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:20:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.05_summits.bed INFO @ Thu, 16 Apr 2020 01:20:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4254 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:20:55: 5000000 INFO @ Thu, 16 Apr 2020 01:20:59: 2000000 INFO @ Thu, 16 Apr 2020 01:21:03: 6000000 INFO @ Thu, 16 Apr 2020 01:21:07: 3000000 INFO @ Thu, 16 Apr 2020 01:21:11: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:21:11: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:21:11: #1 total tags in treatment: 6938958 INFO @ Thu, 16 Apr 2020 01:21:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:11: #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 01:21:11: #1 tags after filtering in treatment: 6938958 INFO @ Thu, 16 Apr 2020 01:21:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:11: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:12: #2 number of paired peaks: 2085 INFO @ Thu, 16 Apr 2020 01:21:12: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:12: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:12: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:12: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:12: #2 predicted fragment length is 98 bps INFO @ Thu, 16 Apr 2020 01:21:12: #2 alternative fragment length(s) may be 98 bps INFO @ Thu, 16 Apr 2020 01:21:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.10_model.r WARNING @ Thu, 16 Apr 2020 01:21:12: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:12: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Thu, 16 Apr 2020 01:21:12: #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 01:21:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:14: 4000000 INFO @ Thu, 16 Apr 2020 01:21:22: 5000000 INFO @ Thu, 16 Apr 2020 01:21:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:29: 6000000 INFO @ Thu, 16 Apr 2020 01:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.10_summits.bed INFO @ Thu, 16 Apr 2020 01:21:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2714 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:21:35: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:21:35: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:21:35: #1 total tags in treatment: 6938958 INFO @ Thu, 16 Apr 2020 01:21:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:35: #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 01:21:35: #1 tags after filtering in treatment: 6938958 INFO @ Thu, 16 Apr 2020 01:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:35: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:36: #2 number of paired peaks: 2085 INFO @ Thu, 16 Apr 2020 01:21:36: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:36: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:36: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:36: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:36: #2 predicted fragment length is 98 bps INFO @ Thu, 16 Apr 2020 01:21:36: #2 alternative fragment length(s) may be 98 bps INFO @ Thu, 16 Apr 2020 01:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.20_model.r WARNING @ Thu, 16 Apr 2020 01:21:36: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:36: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Thu, 16 Apr 2020 01:21:36: #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 01:21:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226977/SRX5226977.20_summits.bed INFO @ Thu, 16 Apr 2020 01:21:58: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1448 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。