Job ID = 5721264 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T21:09:28 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 : 18,573,065 reads read : 37,146,130 reads written : 18,573,065 reads 0-length : 18,573,065 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: 00:05:24 18573065 reads; of these: 18573065 (100.00%) were unpaired; of these: 2840686 (15.29%) aligned 0 times 11120458 (59.87%) aligned exactly 1 time 4611921 (24.83%) aligned >1 times 84.71% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 9656298 / 15732379 = 0.6138 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 06:21:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.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 06:21:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:21:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:21:09: 1000000 INFO @ Thu, 16 Apr 2020 06:21:14: 2000000 INFO @ Thu, 16 Apr 2020 06:21:19: 3000000 INFO @ Thu, 16 Apr 2020 06:21:24: 4000000 INFO @ Thu, 16 Apr 2020 06:21:30: 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 06:21:35: 6000000 INFO @ Thu, 16 Apr 2020 06:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.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 06:21:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:21:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:21:35: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:21:35: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:21:35: #1 total tags in treatment: 6076081 INFO @ Thu, 16 Apr 2020 06:21:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:21:35: #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 06:21:35: #1 tags after filtering in treatment: 6076081 INFO @ Thu, 16 Apr 2020 06:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:21:35: #1 finished! INFO @ Thu, 16 Apr 2020 06:21:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:21:36: #2 number of paired peaks: 426 WARNING @ Thu, 16 Apr 2020 06:21:36: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Thu, 16 Apr 2020 06:21:36: start model_add_line... INFO @ Thu, 16 Apr 2020 06:21:36: start X-correlation... INFO @ Thu, 16 Apr 2020 06:21:36: end of X-cor INFO @ Thu, 16 Apr 2020 06:21:36: #2 finished! INFO @ Thu, 16 Apr 2020 06:21:36: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 06:21:36: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 06:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.05_model.r WARNING @ Thu, 16 Apr 2020 06:21:36: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:21:36: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 06:21:36: #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 06:21:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:21:40: 1000000 INFO @ Thu, 16 Apr 2020 06:21:45: 2000000 INFO @ Thu, 16 Apr 2020 06:21:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:21:50: 3000000 INFO @ Thu, 16 Apr 2020 06:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.05_summits.bed INFO @ Thu, 16 Apr 2020 06:21:55: Done! INFO @ Thu, 16 Apr 2020 06:21:56: 4000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1584 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:22:01: 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 06:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.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 06:22:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:22:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:22:06: 6000000 INFO @ Thu, 16 Apr 2020 06:22:06: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:22:06: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:22:06: #1 total tags in treatment: 6076081 INFO @ Thu, 16 Apr 2020 06:22:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:22:06: #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 06:22:07: #1 tags after filtering in treatment: 6076081 INFO @ Thu, 16 Apr 2020 06:22:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:22:07: #1 finished! INFO @ Thu, 16 Apr 2020 06:22:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:22:07: #2 number of paired peaks: 426 WARNING @ Thu, 16 Apr 2020 06:22:07: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Thu, 16 Apr 2020 06:22:07: start model_add_line... INFO @ Thu, 16 Apr 2020 06:22:07: start X-correlation... INFO @ Thu, 16 Apr 2020 06:22:07: end of X-cor INFO @ Thu, 16 Apr 2020 06:22:07: #2 finished! INFO @ Thu, 16 Apr 2020 06:22:07: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 06:22:07: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 06:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.10_model.r WARNING @ Thu, 16 Apr 2020 06:22:07: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:22:07: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 06:22:07: #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 06:22:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:22:10: 1000000 INFO @ Thu, 16 Apr 2020 06:22:16: 2000000 INFO @ Thu, 16 Apr 2020 06:22:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:22:21: 3000000 INFO @ Thu, 16 Apr 2020 06:22:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:22:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:22:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.10_summits.bed INFO @ Thu, 16 Apr 2020 06:22:26: Done! INFO @ Thu, 16 Apr 2020 06:22:27: 4000000 pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (968 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:22:32: 5000000 INFO @ Thu, 16 Apr 2020 06:22:37: 6000000 INFO @ Thu, 16 Apr 2020 06:22:37: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:22:37: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:22:37: #1 total tags in treatment: 6076081 INFO @ Thu, 16 Apr 2020 06:22:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:22:37: #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 06:22:38: #1 tags after filtering in treatment: 6076081 INFO @ Thu, 16 Apr 2020 06:22:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:22:38: #1 finished! INFO @ Thu, 16 Apr 2020 06:22:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:22:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:22:38: #2 number of paired peaks: 426 WARNING @ Thu, 16 Apr 2020 06:22:38: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Thu, 16 Apr 2020 06:22:38: start model_add_line... INFO @ Thu, 16 Apr 2020 06:22:38: start X-correlation... INFO @ Thu, 16 Apr 2020 06:22:38: end of X-cor INFO @ Thu, 16 Apr 2020 06:22:38: #2 finished! INFO @ Thu, 16 Apr 2020 06:22:38: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 06:22:38: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 06:22:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.20_model.r WARNING @ Thu, 16 Apr 2020 06:22:38: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:22:38: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 06:22:38: #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 06:22:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:22:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:22:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277040/SRX7277040.20_summits.bed INFO @ Thu, 16 Apr 2020 06:22:57: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (510 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。