Job ID = 5721164 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T20:23:42 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 : 15,479,041 reads read : 30,958,082 reads written : 15,479,041 reads 0-length : 15,479,041 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: 00:04:54 15479041 reads; of these: 15479041 (100.00%) were unpaired; of these: 7494464 (48.42%) aligned 0 times 5451072 (35.22%) aligned exactly 1 time 2533505 (16.37%) aligned >1 times 51.58% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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] 793892 / 7984577 = 0.0994 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 05:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.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 05:38:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:38:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:38:06: 1000000 INFO @ Thu, 16 Apr 2020 05:38:11: 2000000 INFO @ Thu, 16 Apr 2020 05:38:17: 3000000 INFO @ Thu, 16 Apr 2020 05:38:22: 4000000 INFO @ Thu, 16 Apr 2020 05:38:27: 5000000 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 05:38:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.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 05:38:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:38:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:38:32: 6000000 INFO @ Thu, 16 Apr 2020 05:38:37: 1000000 INFO @ Thu, 16 Apr 2020 05:38:37: 7000000 INFO @ Thu, 16 Apr 2020 05:38:38: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:38:38: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:38:38: #1 total tags in treatment: 7190685 INFO @ Thu, 16 Apr 2020 05:38:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:38:38: #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 05:38:38: #1 tags after filtering in treatment: 7190685 INFO @ Thu, 16 Apr 2020 05:38:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:38:38: #1 finished! INFO @ Thu, 16 Apr 2020 05:38:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:38:39: #2 number of paired peaks: 1074 INFO @ Thu, 16 Apr 2020 05:38:39: start model_add_line... INFO @ Thu, 16 Apr 2020 05:38:39: start X-correlation... INFO @ Thu, 16 Apr 2020 05:38:39: end of X-cor INFO @ Thu, 16 Apr 2020 05:38:39: #2 finished! INFO @ Thu, 16 Apr 2020 05:38:39: #2 predicted fragment length is 79 bps INFO @ Thu, 16 Apr 2020 05:38:39: #2 alternative fragment length(s) may be 4,79 bps INFO @ Thu, 16 Apr 2020 05:38:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.05_model.r WARNING @ Thu, 16 Apr 2020 05:38:39: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:38:39: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Thu, 16 Apr 2020 05:38:39: #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 05:38:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:38:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:38:42: 2000000 INFO @ Thu, 16 Apr 2020 05:38:47: 3000000 INFO @ Thu, 16 Apr 2020 05:38:52: 4000000 INFO @ Thu, 16 Apr 2020 05:38:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:38:58: 5000000 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 05:39:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.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 05:39:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:39:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:39:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:39:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:39:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.05_summits.bed INFO @ Thu, 16 Apr 2020 05:39:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1871 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:39:03: 6000000 INFO @ Thu, 16 Apr 2020 05:39:06: 1000000 INFO @ Thu, 16 Apr 2020 05:39:08: 7000000 INFO @ Thu, 16 Apr 2020 05:39:09: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:39:09: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:39:09: #1 total tags in treatment: 7190685 INFO @ Thu, 16 Apr 2020 05:39:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:39:09: #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 05:39:09: #1 tags after filtering in treatment: 7190685 INFO @ Thu, 16 Apr 2020 05:39:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:39:09: #1 finished! INFO @ Thu, 16 Apr 2020 05:39:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:39:10: #2 number of paired peaks: 1074 INFO @ Thu, 16 Apr 2020 05:39:10: start model_add_line... INFO @ Thu, 16 Apr 2020 05:39:10: start X-correlation... INFO @ Thu, 16 Apr 2020 05:39:10: end of X-cor INFO @ Thu, 16 Apr 2020 05:39:10: #2 finished! INFO @ Thu, 16 Apr 2020 05:39:10: #2 predicted fragment length is 79 bps INFO @ Thu, 16 Apr 2020 05:39:10: #2 alternative fragment length(s) may be 4,79 bps INFO @ Thu, 16 Apr 2020 05:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.10_model.r WARNING @ Thu, 16 Apr 2020 05:39:10: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:39:10: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Thu, 16 Apr 2020 05:39:10: #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 05:39:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:39:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:39:12: 2000000 INFO @ Thu, 16 Apr 2020 05:39:17: 3000000 INFO @ Thu, 16 Apr 2020 05:39:22: 4000000 INFO @ Thu, 16 Apr 2020 05:39:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:39:27: 5000000 INFO @ Thu, 16 Apr 2020 05:39:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:39:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:39:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.10_summits.bed INFO @ Thu, 16 Apr 2020 05:39:32: Done! INFO @ Thu, 16 Apr 2020 05:39:32: 6000000 pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1116 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:39:37: 7000000 INFO @ Thu, 16 Apr 2020 05:39:38: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:39:38: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:39:38: #1 total tags in treatment: 7190685 INFO @ Thu, 16 Apr 2020 05:39:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:39:38: #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 05:39:39: #1 tags after filtering in treatment: 7190685 INFO @ Thu, 16 Apr 2020 05:39:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:39:39: #1 finished! INFO @ Thu, 16 Apr 2020 05:39:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:39:39: #2 number of paired peaks: 1074 INFO @ Thu, 16 Apr 2020 05:39:39: start model_add_line... INFO @ Thu, 16 Apr 2020 05:39:39: start X-correlation... INFO @ Thu, 16 Apr 2020 05:39:39: end of X-cor INFO @ Thu, 16 Apr 2020 05:39:39: #2 finished! INFO @ Thu, 16 Apr 2020 05:39:39: #2 predicted fragment length is 79 bps INFO @ Thu, 16 Apr 2020 05:39:39: #2 alternative fragment length(s) may be 4,79 bps INFO @ Thu, 16 Apr 2020 05:39:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.20_model.r WARNING @ Thu, 16 Apr 2020 05:39:39: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:39:39: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Thu, 16 Apr 2020 05:39:39: #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 05:39:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:39:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:40:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:40:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:40:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747982/SRX6747982.20_summits.bed INFO @ Thu, 16 Apr 2020 05:40:02: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。