Job ID = 5721190 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T20:35:09 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 ) 2020-04-15T20:36:19 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 ) 2020-04-15T20:36:19 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 ) 2020-04-15T20:36:19 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 ) 2020-04-15T20:36:19 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 : 10,843,975 reads read : 10,843,975 reads written : 10,843,975 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: 00:03:06 10843975 reads; of these: 10843975 (100.00%) were unpaired; of these: 2711997 (25.01%) aligned 0 times 5547536 (51.16%) aligned exactly 1 time 2584442 (23.83%) aligned >1 times 74.99% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 1090911 / 8131978 = 0.1342 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 05:42:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.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 05:42:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:42:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:42:58: 1000000 INFO @ Thu, 16 Apr 2020 05:43:03: 2000000 INFO @ Thu, 16 Apr 2020 05:43:07: 3000000 INFO @ Thu, 16 Apr 2020 05:43:12: 4000000 INFO @ Thu, 16 Apr 2020 05:43:17: 5000000 INFO @ Thu, 16 Apr 2020 05:43:21: 6000000 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 05:43:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.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 05:43:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:43:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:43:26: 7000000 INFO @ Thu, 16 Apr 2020 05:43:26: #1 tag size is determined as 44 bps INFO @ Thu, 16 Apr 2020 05:43:26: #1 tag size = 44 INFO @ Thu, 16 Apr 2020 05:43:26: #1 total tags in treatment: 7041067 INFO @ Thu, 16 Apr 2020 05:43:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:43:26: #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 05:43:26: #1 tags after filtering in treatment: 7041067 INFO @ Thu, 16 Apr 2020 05:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:43:26: #1 finished! INFO @ Thu, 16 Apr 2020 05:43:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:43:27: #2 number of paired peaks: 588 WARNING @ Thu, 16 Apr 2020 05:43:27: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Thu, 16 Apr 2020 05:43:27: start model_add_line... INFO @ Thu, 16 Apr 2020 05:43:27: start X-correlation... INFO @ Thu, 16 Apr 2020 05:43:27: end of X-cor INFO @ Thu, 16 Apr 2020 05:43:27: #2 finished! INFO @ Thu, 16 Apr 2020 05:43:27: #2 predicted fragment length is 58 bps INFO @ Thu, 16 Apr 2020 05:43:27: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 16 Apr 2020 05:43:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.05_model.r WARNING @ Thu, 16 Apr 2020 05:43:27: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:43:27: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 16 Apr 2020 05:43:27: #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 05:43:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:43:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:43:28: 1000000 INFO @ Thu, 16 Apr 2020 05:43:33: 2000000 INFO @ Thu, 16 Apr 2020 05:43:38: 3000000 INFO @ Thu, 16 Apr 2020 05:43:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:43:42: 4000000 INFO @ Thu, 16 Apr 2020 05:43:47: 5000000 INFO @ Thu, 16 Apr 2020 05:43:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:43:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:43:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.05_summits.bed INFO @ Thu, 16 Apr 2020 05:43:48: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1502 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 05:43:52: 6000000 INFO @ Thu, 16 Apr 2020 05:43:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.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 05:43:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:43:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:43:57: 7000000 INFO @ Thu, 16 Apr 2020 05:43:57: #1 tag size is determined as 44 bps INFO @ Thu, 16 Apr 2020 05:43:57: #1 tag size = 44 INFO @ Thu, 16 Apr 2020 05:43:57: #1 total tags in treatment: 7041067 INFO @ Thu, 16 Apr 2020 05:43:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:43:57: #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 05:43:57: #1 tags after filtering in treatment: 7041067 INFO @ Thu, 16 Apr 2020 05:43:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:43:57: #1 finished! INFO @ Thu, 16 Apr 2020 05:43:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:43:58: #2 number of paired peaks: 588 WARNING @ Thu, 16 Apr 2020 05:43:58: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Thu, 16 Apr 2020 05:43:58: start model_add_line... INFO @ Thu, 16 Apr 2020 05:43:58: start X-correlation... INFO @ Thu, 16 Apr 2020 05:43:58: end of X-cor INFO @ Thu, 16 Apr 2020 05:43:58: #2 finished! INFO @ Thu, 16 Apr 2020 05:43:58: #2 predicted fragment length is 58 bps INFO @ Thu, 16 Apr 2020 05:43:58: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 16 Apr 2020 05:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.10_model.r WARNING @ Thu, 16 Apr 2020 05:43:58: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:43:58: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 16 Apr 2020 05:43:58: #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 05:43:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:43:58: 1000000 INFO @ Thu, 16 Apr 2020 05:44:03: 2000000 INFO @ Thu, 16 Apr 2020 05:44:08: 3000000 INFO @ Thu, 16 Apr 2020 05:44:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:44:12: 4000000 INFO @ Thu, 16 Apr 2020 05:44:17: 5000000 INFO @ Thu, 16 Apr 2020 05:44:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:44:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:44:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.10_summits.bed INFO @ Thu, 16 Apr 2020 05:44:19: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1303 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:44:22: 6000000 INFO @ Thu, 16 Apr 2020 05:44:27: 7000000 INFO @ Thu, 16 Apr 2020 05:44:27: #1 tag size is determined as 44 bps INFO @ Thu, 16 Apr 2020 05:44:27: #1 tag size = 44 INFO @ Thu, 16 Apr 2020 05:44:27: #1 total tags in treatment: 7041067 INFO @ Thu, 16 Apr 2020 05:44:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:44:27: #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 05:44:27: #1 tags after filtering in treatment: 7041067 INFO @ Thu, 16 Apr 2020 05:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:44:27: #1 finished! INFO @ Thu, 16 Apr 2020 05:44:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:44:27: #2 number of paired peaks: 588 WARNING @ Thu, 16 Apr 2020 05:44:27: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Thu, 16 Apr 2020 05:44:27: start model_add_line... INFO @ Thu, 16 Apr 2020 05:44:27: start X-correlation... INFO @ Thu, 16 Apr 2020 05:44:27: end of X-cor INFO @ Thu, 16 Apr 2020 05:44:27: #2 finished! INFO @ Thu, 16 Apr 2020 05:44:27: #2 predicted fragment length is 58 bps INFO @ Thu, 16 Apr 2020 05:44:27: #2 alternative fragment length(s) may be 58 bps INFO @ Thu, 16 Apr 2020 05:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.20_model.r WARNING @ Thu, 16 Apr 2020 05:44:27: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:44:27: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Thu, 16 Apr 2020 05:44:27: #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 05:44:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:44:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:44:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:44:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:44:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6780072/SRX6780072.20_summits.bed INFO @ Thu, 16 Apr 2020 05:44:49: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (962 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。