Job ID = 5720731 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:05:24 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 ) 2020-04-15T16:05:24 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 ) 2020-04-15T16:06:33 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 : 13,325,589 reads read : 26,651,178 reads written : 13,325,589 reads 0-length : 13,325,589 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: 00:05:04 13325589 reads; of these: 13325589 (100.00%) were unpaired; of these: 850636 (6.38%) aligned 0 times 9278108 (69.63%) aligned exactly 1 time 3196845 (23.99%) aligned >1 times 93.62% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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 8 files... [bam_rmdupse_core] 1011887 / 12474953 = 0.0811 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 01:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.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 01:19:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:19:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:19:44: 1000000 INFO @ Thu, 16 Apr 2020 01:19:51: 2000000 INFO @ Thu, 16 Apr 2020 01:19:57: 3000000 INFO @ Thu, 16 Apr 2020 01:20:04: 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 01:20:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.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 01:20:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:20:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:20:10: 5000000 INFO @ Thu, 16 Apr 2020 01:20:15: 1000000 INFO @ Thu, 16 Apr 2020 01:20:17: 6000000 INFO @ Thu, 16 Apr 2020 01:20:22: 2000000 INFO @ Thu, 16 Apr 2020 01:20:23: 7000000 INFO @ Thu, 16 Apr 2020 01:20:29: 3000000 INFO @ Thu, 16 Apr 2020 01:20:30: 8000000 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 01:20:36: 4000000 INFO @ Thu, 16 Apr 2020 01:20:37: 9000000 INFO @ Thu, 16 Apr 2020 01:20:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.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 01:20:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:20:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:20:43: 10000000 INFO @ Thu, 16 Apr 2020 01:20:43: 5000000 INFO @ Thu, 16 Apr 2020 01:20:45: 1000000 INFO @ Thu, 16 Apr 2020 01:20:50: 11000000 INFO @ Thu, 16 Apr 2020 01:20:50: 6000000 INFO @ Thu, 16 Apr 2020 01:20:52: 2000000 INFO @ Thu, 16 Apr 2020 01:20:53: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:20:53: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:20:53: #1 total tags in treatment: 11463066 INFO @ Thu, 16 Apr 2020 01:20:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:20:53: #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 01:20:53: #1 tags after filtering in treatment: 11463066 INFO @ Thu, 16 Apr 2020 01:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:20:53: #1 finished! INFO @ Thu, 16 Apr 2020 01:20:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:20:54: #2 number of paired peaks: 685 WARNING @ Thu, 16 Apr 2020 01:20:54: Fewer paired peaks (685) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 685 pairs to build model! INFO @ Thu, 16 Apr 2020 01:20:54: start model_add_line... INFO @ Thu, 16 Apr 2020 01:20:54: start X-correlation... INFO @ Thu, 16 Apr 2020 01:20:54: end of X-cor INFO @ Thu, 16 Apr 2020 01:20:54: #2 finished! INFO @ Thu, 16 Apr 2020 01:20:54: #2 predicted fragment length is 86 bps INFO @ Thu, 16 Apr 2020 01:20:54: #2 alternative fragment length(s) may be 86 bps INFO @ Thu, 16 Apr 2020 01:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.05_model.r WARNING @ Thu, 16 Apr 2020 01:20:54: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:20:54: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Thu, 16 Apr 2020 01:20:54: #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 01:20:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:20:57: 7000000 INFO @ Thu, 16 Apr 2020 01:20:59: 3000000 INFO @ Thu, 16 Apr 2020 01:21:04: 8000000 INFO @ Thu, 16 Apr 2020 01:21:06: 4000000 INFO @ Thu, 16 Apr 2020 01:21:10: 9000000 INFO @ Thu, 16 Apr 2020 01:21:13: 5000000 INFO @ Thu, 16 Apr 2020 01:21:17: 10000000 INFO @ Thu, 16 Apr 2020 01:21:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:20: 6000000 INFO @ Thu, 16 Apr 2020 01:21:24: 11000000 INFO @ Thu, 16 Apr 2020 01:21:26: 7000000 INFO @ Thu, 16 Apr 2020 01:21:27: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:21:27: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:21:27: #1 total tags in treatment: 11463066 INFO @ Thu, 16 Apr 2020 01:21:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:27: #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 01:21:27: #1 tags after filtering in treatment: 11463066 INFO @ Thu, 16 Apr 2020 01:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:27: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:28: #2 number of paired peaks: 685 WARNING @ Thu, 16 Apr 2020 01:21:28: Fewer paired peaks (685) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 685 pairs to build model! INFO @ Thu, 16 Apr 2020 01:21:28: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:28: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:28: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:28: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:28: #2 predicted fragment length is 86 bps INFO @ Thu, 16 Apr 2020 01:21:28: #2 alternative fragment length(s) may be 86 bps INFO @ Thu, 16 Apr 2020 01:21:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.10_model.r WARNING @ Thu, 16 Apr 2020 01:21:28: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:28: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Thu, 16 Apr 2020 01:21:28: #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 01:21:28: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.05_summits.bed INFO @ Thu, 16 Apr 2020 01:21:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5091 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:21:33: 8000000 INFO @ Thu, 16 Apr 2020 01:21:39: 9000000 INFO @ Thu, 16 Apr 2020 01:21:46: 10000000 INFO @ Thu, 16 Apr 2020 01:21:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:52: 11000000 INFO @ Thu, 16 Apr 2020 01:21:55: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:21:55: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:21:55: #1 total tags in treatment: 11463066 INFO @ Thu, 16 Apr 2020 01:21:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:55: #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 01:21:55: #1 tags after filtering in treatment: 11463066 INFO @ Thu, 16 Apr 2020 01:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:55: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:56: #2 number of paired peaks: 685 WARNING @ Thu, 16 Apr 2020 01:21:56: Fewer paired peaks (685) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 685 pairs to build model! INFO @ Thu, 16 Apr 2020 01:21:56: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:56: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:56: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:56: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:56: #2 predicted fragment length is 86 bps INFO @ Thu, 16 Apr 2020 01:21:56: #2 alternative fragment length(s) may be 86 bps INFO @ Thu, 16 Apr 2020 01:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.20_model.r WARNING @ Thu, 16 Apr 2020 01:21:56: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:56: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Thu, 16 Apr 2020 01:21:56: #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 01:21:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:22:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:22:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:22:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.10_summits.bed INFO @ Thu, 16 Apr 2020 01:22:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1949 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:22:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:22:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:22:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:22:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226971/SRX5226971.20_summits.bed INFO @ Thu, 16 Apr 2020 01:22:31: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (721 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。