Job ID = 5720757 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:16:06 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 ) 2020-04-15T16:16:06 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 ) 2020-04-15T16:16:06 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 : 11,846,198 reads read : 23,692,396 reads written : 11,846,198 reads 0-length : 11,846,198 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: 00:05:02 11846198 reads; of these: 11846198 (100.00%) were unpaired; of these: 2493050 (21.05%) aligned 0 times 6488577 (54.77%) aligned exactly 1 time 2864571 (24.18%) aligned >1 times 78.95% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 926365 / 9353148 = 0.0990 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 01:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.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 01:26:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:26:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:26:23: 1000000 INFO @ Thu, 16 Apr 2020 01:26:28: 2000000 INFO @ Thu, 16 Apr 2020 01:26:34: 3000000 INFO @ Thu, 16 Apr 2020 01:26:39: 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 01:26:45: 5000000 INFO @ Thu, 16 Apr 2020 01:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.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 01:26:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:26:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:26:50: 6000000 INFO @ Thu, 16 Apr 2020 01:26:53: 1000000 INFO @ Thu, 16 Apr 2020 01:26:56: 7000000 INFO @ Thu, 16 Apr 2020 01:26:59: 2000000 INFO @ Thu, 16 Apr 2020 01:27:02: 8000000 INFO @ Thu, 16 Apr 2020 01:27:04: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:27:04: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:27:04: #1 total tags in treatment: 8426783 INFO @ Thu, 16 Apr 2020 01:27:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:27:04: #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 01:27:04: #1 tags after filtering in treatment: 8426783 INFO @ Thu, 16 Apr 2020 01:27:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:27:04: #1 finished! INFO @ Thu, 16 Apr 2020 01:27:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:27:05: 3000000 INFO @ Thu, 16 Apr 2020 01:27:05: #2 number of paired peaks: 958 WARNING @ Thu, 16 Apr 2020 01:27:05: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Thu, 16 Apr 2020 01:27:05: start model_add_line... INFO @ Thu, 16 Apr 2020 01:27:05: start X-correlation... INFO @ Thu, 16 Apr 2020 01:27:05: end of X-cor INFO @ Thu, 16 Apr 2020 01:27:05: #2 finished! INFO @ Thu, 16 Apr 2020 01:27:05: #2 predicted fragment length is 85 bps INFO @ Thu, 16 Apr 2020 01:27:05: #2 alternative fragment length(s) may be 85 bps INFO @ Thu, 16 Apr 2020 01:27:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.05_model.r WARNING @ Thu, 16 Apr 2020 01:27:05: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:27:05: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Thu, 16 Apr 2020 01:27:05: #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 01:27:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:27:10: 4000000 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 01:27:16: 5000000 INFO @ Thu, 16 Apr 2020 01:27:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.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 01:27:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:27:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:27:21: 6000000 INFO @ Thu, 16 Apr 2020 01:27:23: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:27:24: 1000000 INFO @ Thu, 16 Apr 2020 01:27:27: 7000000 INFO @ Thu, 16 Apr 2020 01:27:30: 2000000 INFO @ Thu, 16 Apr 2020 01:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.05_summits.bed INFO @ Thu, 16 Apr 2020 01:27:32: Done! INFO @ Thu, 16 Apr 2020 01:27:33: 8000000 INFO @ Thu, 16 Apr 2020 01:27:35: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:27:35: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:27:35: #1 total tags in treatment: 8426783 INFO @ Thu, 16 Apr 2020 01:27:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:27:35: #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 01:27:35: #1 tags after filtering in treatment: 8426783 INFO @ Thu, 16 Apr 2020 01:27:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:27:35: #1 finished! INFO @ Thu, 16 Apr 2020 01:27:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:27:35: 3000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3532 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:27:36: #2 number of paired peaks: 958 WARNING @ Thu, 16 Apr 2020 01:27:36: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Thu, 16 Apr 2020 01:27:36: start model_add_line... INFO @ Thu, 16 Apr 2020 01:27:36: start X-correlation... INFO @ Thu, 16 Apr 2020 01:27:36: end of X-cor INFO @ Thu, 16 Apr 2020 01:27:36: #2 finished! INFO @ Thu, 16 Apr 2020 01:27:36: #2 predicted fragment length is 85 bps INFO @ Thu, 16 Apr 2020 01:27:36: #2 alternative fragment length(s) may be 85 bps INFO @ Thu, 16 Apr 2020 01:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.10_model.r WARNING @ Thu, 16 Apr 2020 01:27:36: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:27:36: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Thu, 16 Apr 2020 01:27:36: #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 01:27:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:27:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:27:41: 4000000 INFO @ Thu, 16 Apr 2020 01:27:46: 5000000 INFO @ Thu, 16 Apr 2020 01:27:52: 6000000 INFO @ Thu, 16 Apr 2020 01:27:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:27:57: 7000000 INFO @ Thu, 16 Apr 2020 01:28:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:28:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:28:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.10_summits.bed INFO @ Thu, 16 Apr 2020 01:28:01: Done! INFO @ Thu, 16 Apr 2020 01:28:03: 8000000 pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1928 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:28:05: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:28:05: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:28:05: #1 total tags in treatment: 8426783 INFO @ Thu, 16 Apr 2020 01:28:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:28:05: #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 01:28:05: #1 tags after filtering in treatment: 8426783 INFO @ Thu, 16 Apr 2020 01:28:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:28:05: #1 finished! INFO @ Thu, 16 Apr 2020 01:28:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:28:06: #2 number of paired peaks: 958 WARNING @ Thu, 16 Apr 2020 01:28:06: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Thu, 16 Apr 2020 01:28:06: start model_add_line... INFO @ Thu, 16 Apr 2020 01:28:06: start X-correlation... INFO @ Thu, 16 Apr 2020 01:28:06: end of X-cor INFO @ Thu, 16 Apr 2020 01:28:06: #2 finished! INFO @ Thu, 16 Apr 2020 01:28:06: #2 predicted fragment length is 85 bps INFO @ Thu, 16 Apr 2020 01:28:06: #2 alternative fragment length(s) may be 85 bps INFO @ Thu, 16 Apr 2020 01:28:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.20_model.r WARNING @ Thu, 16 Apr 2020 01:28:06: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:28:06: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Thu, 16 Apr 2020 01:28:06: #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 01:28:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:28:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:28:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:28:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:28:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226994/SRX5226994.20_summits.bed INFO @ Thu, 16 Apr 2020 01:28:34: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (801 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。