Job ID = 5721041 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:54:52 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 ) 2020-04-15T19:05:30 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 : 62,392,803 reads read : 62,392,803 reads written : 62,392,803 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: 00:00:01 Multiseed full-index search: 00:13:16 62392803 reads; of these: 62392803 (100.00%) were unpaired; of these: 41441508 (66.42%) aligned 0 times 12809459 (20.53%) aligned exactly 1 time 8141836 (13.05%) aligned >1 times 33.58% overall alignment rate Time searching: 00:13:17 Overall time: 00:13:17 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 12 files... [bam_rmdupse_core] 15238879 / 20951295 = 0.7273 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 04:30:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.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 04:30:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:30:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:30:23: 1000000 INFO @ Thu, 16 Apr 2020 04:30:29: 2000000 INFO @ Thu, 16 Apr 2020 04:30:35: 3000000 INFO @ Thu, 16 Apr 2020 04:30:41: 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 04:30:46: 5000000 INFO @ Thu, 16 Apr 2020 04:30:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.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 04:30:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:30:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:30:51: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 04:30:51: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 04:30:51: #1 total tags in treatment: 5712416 INFO @ Thu, 16 Apr 2020 04:30:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:30:51: #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 04:30:51: #1 tags after filtering in treatment: 5712416 INFO @ Thu, 16 Apr 2020 04:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 04:30:51: #1 finished! INFO @ Thu, 16 Apr 2020 04:30:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:30:51: #2 number of paired peaks: 3161 INFO @ Thu, 16 Apr 2020 04:30:51: start model_add_line... INFO @ Thu, 16 Apr 2020 04:30:51: start X-correlation... INFO @ Thu, 16 Apr 2020 04:30:51: end of X-cor INFO @ Thu, 16 Apr 2020 04:30:51: #2 finished! INFO @ Thu, 16 Apr 2020 04:30:51: #2 predicted fragment length is 63 bps INFO @ Thu, 16 Apr 2020 04:30:51: #2 alternative fragment length(s) may be 63 bps INFO @ Thu, 16 Apr 2020 04:30:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.05_model.r WARNING @ Thu, 16 Apr 2020 04:30:51: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:30:51: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Thu, 16 Apr 2020 04:30:51: #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 04:30:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:30:52: 1000000 INFO @ Thu, 16 Apr 2020 04:30:57: 2000000 INFO @ Thu, 16 Apr 2020 04:31:02: 3000000 INFO @ Thu, 16 Apr 2020 04:31:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:31:07: 4000000 INFO @ Thu, 16 Apr 2020 04:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:31:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:31:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.05_summits.bed INFO @ Thu, 16 Apr 2020 04:31:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6174 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:31:12: 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 04:31:15: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 04:31:15: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 04:31:15: #1 total tags in treatment: 5712416 INFO @ Thu, 16 Apr 2020 04:31:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:31:15: #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 04:31:15: #1 tags after filtering in treatment: 5712416 INFO @ Thu, 16 Apr 2020 04:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 04:31:15: #1 finished! INFO @ Thu, 16 Apr 2020 04:31:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:31:16: #2 number of paired peaks: 3161 INFO @ Thu, 16 Apr 2020 04:31:16: start model_add_line... INFO @ Thu, 16 Apr 2020 04:31:16: start X-correlation... INFO @ Thu, 16 Apr 2020 04:31:16: end of X-cor INFO @ Thu, 16 Apr 2020 04:31:16: #2 finished! INFO @ Thu, 16 Apr 2020 04:31:16: #2 predicted fragment length is 63 bps INFO @ Thu, 16 Apr 2020 04:31:16: #2 alternative fragment length(s) may be 63 bps INFO @ Thu, 16 Apr 2020 04:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.10_model.r WARNING @ Thu, 16 Apr 2020 04:31:16: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:31:16: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Thu, 16 Apr 2020 04:31:16: #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 04:31:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:31:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.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 04:31:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:31:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:31:23: 1000000 INFO @ Thu, 16 Apr 2020 04:31:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:31:28: 2000000 INFO @ Thu, 16 Apr 2020 04:31:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:31:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:31:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.10_summits.bed INFO @ Thu, 16 Apr 2020 04:31:34: Done! INFO @ Thu, 16 Apr 2020 04:31:34: 3000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3972 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:31:39: 4000000 INFO @ Thu, 16 Apr 2020 04:31:45: 5000000 INFO @ Thu, 16 Apr 2020 04:31:50: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 04:31:50: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 04:31:50: #1 total tags in treatment: 5712416 INFO @ Thu, 16 Apr 2020 04:31:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:31:50: #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 04:31:50: #1 tags after filtering in treatment: 5712416 INFO @ Thu, 16 Apr 2020 04:31:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 04:31:50: #1 finished! INFO @ Thu, 16 Apr 2020 04:31:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:31:50: #2 number of paired peaks: 3161 INFO @ Thu, 16 Apr 2020 04:31:50: start model_add_line... INFO @ Thu, 16 Apr 2020 04:31:50: start X-correlation... INFO @ Thu, 16 Apr 2020 04:31:50: end of X-cor INFO @ Thu, 16 Apr 2020 04:31:50: #2 finished! INFO @ Thu, 16 Apr 2020 04:31:50: #2 predicted fragment length is 63 bps INFO @ Thu, 16 Apr 2020 04:31:50: #2 alternative fragment length(s) may be 63 bps INFO @ Thu, 16 Apr 2020 04:31:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.20_model.r WARNING @ Thu, 16 Apr 2020 04:31:50: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:31:50: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Thu, 16 Apr 2020 04:31:50: #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 04:31:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:32:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:32:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:32:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:32:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386775/SRX6386775.20_summits.bed INFO @ Thu, 16 Apr 2020 04:32:10: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1718 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。