Job ID = 5721209 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T20:48:19 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 ) 2020-04-15T20:48:19 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 ) 1900-01-00T00:00:00 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 ) 2020-04-15T20:48:19 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 ) 2020-04-15T20:48:19 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 ) 2020-04-15T20:57:09 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 ) spots read : 21,937,641 reads read : 21,937,641 reads written : 21,937,641 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: 00:07:48 21937641 reads; of these: 21937641 (100.00%) were unpaired; of these: 743077 (3.39%) aligned 0 times 14583032 (66.47%) aligned exactly 1 time 6611532 (30.14%) aligned >1 times 96.61% overall alignment rate Time searching: 00:07:48 Overall time: 00:07:48 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] 3281437 / 21194564 = 0.1548 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 06:10:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.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 06:10:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:10:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:10:43: 1000000 INFO @ Thu, 16 Apr 2020 06:10:48: 2000000 INFO @ Thu, 16 Apr 2020 06:10:53: 3000000 INFO @ Thu, 16 Apr 2020 06:10:57: 4000000 INFO @ Thu, 16 Apr 2020 06:11:02: 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 06:11:07: 6000000 INFO @ Thu, 16 Apr 2020 06:11:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.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 06:11:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:11:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:11:12: 7000000 INFO @ Thu, 16 Apr 2020 06:11:13: 1000000 INFO @ Thu, 16 Apr 2020 06:11:16: 8000000 INFO @ Thu, 16 Apr 2020 06:11:18: 2000000 INFO @ Thu, 16 Apr 2020 06:11:21: 9000000 INFO @ Thu, 16 Apr 2020 06:11:23: 3000000 INFO @ Thu, 16 Apr 2020 06:11:26: 10000000 INFO @ Thu, 16 Apr 2020 06:11:27: 4000000 INFO @ Thu, 16 Apr 2020 06:11:31: 11000000 INFO @ Thu, 16 Apr 2020 06:11:32: 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 06:11:36: 12000000 INFO @ Thu, 16 Apr 2020 06:11:37: 6000000 INFO @ Thu, 16 Apr 2020 06:11:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.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 06:11:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:11:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:11:41: 13000000 INFO @ Thu, 16 Apr 2020 06:11:42: 7000000 INFO @ Thu, 16 Apr 2020 06:11:43: 1000000 INFO @ Thu, 16 Apr 2020 06:11:46: 14000000 INFO @ Thu, 16 Apr 2020 06:11:47: 8000000 INFO @ Thu, 16 Apr 2020 06:11:48: 2000000 INFO @ Thu, 16 Apr 2020 06:11:51: 15000000 INFO @ Thu, 16 Apr 2020 06:11:52: 9000000 INFO @ Thu, 16 Apr 2020 06:11:53: 3000000 INFO @ Thu, 16 Apr 2020 06:11:55: 16000000 INFO @ Thu, 16 Apr 2020 06:11:57: 10000000 INFO @ Thu, 16 Apr 2020 06:11:58: 4000000 INFO @ Thu, 16 Apr 2020 06:12:00: 17000000 INFO @ Thu, 16 Apr 2020 06:12:02: 11000000 INFO @ Thu, 16 Apr 2020 06:12:03: 5000000 INFO @ Thu, 16 Apr 2020 06:12:05: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:12:05: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:12:05: #1 total tags in treatment: 17913127 INFO @ Thu, 16 Apr 2020 06:12:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:12:05: #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 06:12:05: #1 tags after filtering in treatment: 17913127 INFO @ Thu, 16 Apr 2020 06:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:12:05: #1 finished! INFO @ Thu, 16 Apr 2020 06:12:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:12:06: #2 number of paired peaks: 491 WARNING @ Thu, 16 Apr 2020 06:12:06: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Thu, 16 Apr 2020 06:12:06: start model_add_line... INFO @ Thu, 16 Apr 2020 06:12:07: start X-correlation... INFO @ Thu, 16 Apr 2020 06:12:07: end of X-cor INFO @ Thu, 16 Apr 2020 06:12:07: #2 finished! INFO @ Thu, 16 Apr 2020 06:12:07: #2 predicted fragment length is 46 bps INFO @ Thu, 16 Apr 2020 06:12:07: #2 alternative fragment length(s) may be 46 bps INFO @ Thu, 16 Apr 2020 06:12:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.05_model.r WARNING @ Thu, 16 Apr 2020 06:12:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:12:07: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Thu, 16 Apr 2020 06:12:07: #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 06:12:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:12:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:12:07: 12000000 INFO @ Thu, 16 Apr 2020 06:12:08: 6000000 INFO @ Thu, 16 Apr 2020 06:12:12: 13000000 INFO @ Thu, 16 Apr 2020 06:12:13: 7000000 INFO @ Thu, 16 Apr 2020 06:12:16: 14000000 INFO @ Thu, 16 Apr 2020 06:12:18: 8000000 INFO @ Thu, 16 Apr 2020 06:12:21: 15000000 INFO @ Thu, 16 Apr 2020 06:12:23: 9000000 INFO @ Thu, 16 Apr 2020 06:12:26: 16000000 INFO @ Thu, 16 Apr 2020 06:12:27: 10000000 INFO @ Thu, 16 Apr 2020 06:12:31: 17000000 INFO @ Thu, 16 Apr 2020 06:12:32: 11000000 INFO @ Thu, 16 Apr 2020 06:12:36: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:12:36: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:12:36: #1 total tags in treatment: 17913127 INFO @ Thu, 16 Apr 2020 06:12:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:12:36: #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 06:12:36: #1 tags after filtering in treatment: 17913127 INFO @ Thu, 16 Apr 2020 06:12:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:12:36: #1 finished! INFO @ Thu, 16 Apr 2020 06:12:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:12:37: #2 number of paired peaks: 491 WARNING @ Thu, 16 Apr 2020 06:12:37: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Thu, 16 Apr 2020 06:12:37: start model_add_line... INFO @ Thu, 16 Apr 2020 06:12:37: 12000000 INFO @ Thu, 16 Apr 2020 06:12:37: start X-correlation... INFO @ Thu, 16 Apr 2020 06:12:37: end of X-cor INFO @ Thu, 16 Apr 2020 06:12:37: #2 finished! INFO @ Thu, 16 Apr 2020 06:12:37: #2 predicted fragment length is 46 bps INFO @ Thu, 16 Apr 2020 06:12:37: #2 alternative fragment length(s) may be 46 bps INFO @ Thu, 16 Apr 2020 06:12:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.10_model.r WARNING @ Thu, 16 Apr 2020 06:12:37: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:12:37: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Thu, 16 Apr 2020 06:12:37: #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 06:12:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:12:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:12:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:12:42: 13000000 INFO @ Thu, 16 Apr 2020 06:12:47: 14000000 INFO @ Thu, 16 Apr 2020 06:12:52: 15000000 INFO @ Thu, 16 Apr 2020 06:12:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:12:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:12:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.05_summits.bed INFO @ Thu, 16 Apr 2020 06:12:56: Done! INFO @ Thu, 16 Apr 2020 06:12:57: 16000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3245 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:13:01: 17000000 INFO @ Thu, 16 Apr 2020 06:13:06: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:13:06: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:13:06: #1 total tags in treatment: 17913127 INFO @ Thu, 16 Apr 2020 06:13:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:13:06: #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 06:13:06: #1 tags after filtering in treatment: 17913127 INFO @ Thu, 16 Apr 2020 06:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:13:06: #1 finished! INFO @ Thu, 16 Apr 2020 06:13:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:13:07: #2 number of paired peaks: 491 WARNING @ Thu, 16 Apr 2020 06:13:07: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Thu, 16 Apr 2020 06:13:07: start model_add_line... INFO @ Thu, 16 Apr 2020 06:13:07: start X-correlation... INFO @ Thu, 16 Apr 2020 06:13:08: end of X-cor INFO @ Thu, 16 Apr 2020 06:13:08: #2 finished! INFO @ Thu, 16 Apr 2020 06:13:08: #2 predicted fragment length is 46 bps INFO @ Thu, 16 Apr 2020 06:13:08: #2 alternative fragment length(s) may be 46 bps INFO @ Thu, 16 Apr 2020 06:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.20_model.r WARNING @ Thu, 16 Apr 2020 06:13:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:13:08: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Thu, 16 Apr 2020 06:13:08: #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 06:13:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:13:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:13:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:13:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:13:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.10_summits.bed INFO @ Thu, 16 Apr 2020 06:13:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2224 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:13:43: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:13:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:13:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:13:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827673/SRX6827673.20_summits.bed INFO @ Thu, 16 Apr 2020 06:13:59: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1232 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。