Job ID = 5721163 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T20:23:36 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 ) 2020-04-15T20:25:51 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 ) 2020-04-15T20:25:51 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 ) 2020-04-15T20:25:51 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 ) 2020-04-15T20:25:51 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 ) 2020-04-15T20:27:01 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 ) 2020-04-15T20:27:01 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 : 19,970,393 reads read : 39,940,786 reads written : 19,970,393 reads 0-length : 19,970,393 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: 00:07:38 19970393 reads; of these: 19970393 (100.00%) were unpaired; of these: 397578 (1.99%) aligned 0 times 14399346 (72.10%) aligned exactly 1 time 5173469 (25.91%) aligned >1 times 98.01% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 1848718 / 19572815 = 0.0945 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 05:46:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.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 05:46:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:46:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:46:21: 1000000 INFO @ Thu, 16 Apr 2020 05:46:26: 2000000 INFO @ Thu, 16 Apr 2020 05:46:31: 3000000 INFO @ Thu, 16 Apr 2020 05:46:36: 4000000 INFO @ Thu, 16 Apr 2020 05:46:41: 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 05:46:46: 6000000 INFO @ Thu, 16 Apr 2020 05:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.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 05:46:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:46:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:46:51: 7000000 INFO @ Thu, 16 Apr 2020 05:46:52: 1000000 INFO @ Thu, 16 Apr 2020 05:46:57: 8000000 INFO @ Thu, 16 Apr 2020 05:46:57: 2000000 INFO @ Thu, 16 Apr 2020 05:47:02: 9000000 INFO @ Thu, 16 Apr 2020 05:47:03: 3000000 INFO @ Thu, 16 Apr 2020 05:47:07: 10000000 INFO @ Thu, 16 Apr 2020 05:47:08: 4000000 INFO @ Thu, 16 Apr 2020 05:47:12: 11000000 INFO @ Thu, 16 Apr 2020 05:47:13: 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 05:47:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.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 05:47:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:47:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:47:18: 12000000 INFO @ Thu, 16 Apr 2020 05:47:18: 6000000 INFO @ Thu, 16 Apr 2020 05:47:22: 1000000 INFO @ Thu, 16 Apr 2020 05:47:23: 13000000 INFO @ Thu, 16 Apr 2020 05:47:23: 7000000 INFO @ Thu, 16 Apr 2020 05:47:27: 2000000 INFO @ Thu, 16 Apr 2020 05:47:28: 14000000 INFO @ Thu, 16 Apr 2020 05:47:29: 8000000 INFO @ Thu, 16 Apr 2020 05:47:33: 3000000 INFO @ Thu, 16 Apr 2020 05:47:34: 9000000 INFO @ Thu, 16 Apr 2020 05:47:34: 15000000 INFO @ Thu, 16 Apr 2020 05:47:38: 4000000 INFO @ Thu, 16 Apr 2020 05:47:39: 10000000 INFO @ Thu, 16 Apr 2020 05:47:39: 16000000 INFO @ Thu, 16 Apr 2020 05:47:43: 5000000 INFO @ Thu, 16 Apr 2020 05:47:44: 11000000 INFO @ Thu, 16 Apr 2020 05:47:45: 17000000 INFO @ Thu, 16 Apr 2020 05:47:49: #1 tag size is determined as 73 bps INFO @ Thu, 16 Apr 2020 05:47:49: #1 tag size = 73 INFO @ Thu, 16 Apr 2020 05:47:49: #1 total tags in treatment: 17724097 INFO @ Thu, 16 Apr 2020 05:47:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:47:49: #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 05:47:49: 6000000 INFO @ Thu, 16 Apr 2020 05:47:49: #1 tags after filtering in treatment: 17724097 INFO @ Thu, 16 Apr 2020 05:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:47:49: #1 finished! INFO @ Thu, 16 Apr 2020 05:47:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:47:50: 12000000 INFO @ Thu, 16 Apr 2020 05:47:50: #2 number of paired peaks: 519 WARNING @ Thu, 16 Apr 2020 05:47:50: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Thu, 16 Apr 2020 05:47:50: start model_add_line... INFO @ Thu, 16 Apr 2020 05:47:50: start X-correlation... INFO @ Thu, 16 Apr 2020 05:47:50: end of X-cor INFO @ Thu, 16 Apr 2020 05:47:50: #2 finished! INFO @ Thu, 16 Apr 2020 05:47:50: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 05:47:50: #2 alternative fragment length(s) may be 3,78 bps INFO @ Thu, 16 Apr 2020 05:47:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.05_model.r WARNING @ Thu, 16 Apr 2020 05:47:50: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:47:50: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Thu, 16 Apr 2020 05:47:50: #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 05:47:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:47:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:47:54: 7000000 INFO @ Thu, 16 Apr 2020 05:47:55: 13000000 INFO @ Thu, 16 Apr 2020 05:47:59: 8000000 INFO @ Thu, 16 Apr 2020 05:48:00: 14000000 INFO @ Thu, 16 Apr 2020 05:48:04: 9000000 INFO @ Thu, 16 Apr 2020 05:48:05: 15000000 INFO @ Thu, 16 Apr 2020 05:48:10: 10000000 INFO @ Thu, 16 Apr 2020 05:48:11: 16000000 INFO @ Thu, 16 Apr 2020 05:48:15: 11000000 INFO @ Thu, 16 Apr 2020 05:48:16: 17000000 INFO @ Thu, 16 Apr 2020 05:48:20: #1 tag size is determined as 73 bps INFO @ Thu, 16 Apr 2020 05:48:20: #1 tag size = 73 INFO @ Thu, 16 Apr 2020 05:48:20: #1 total tags in treatment: 17724097 INFO @ Thu, 16 Apr 2020 05:48:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:48:20: #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 05:48:20: #1 tags after filtering in treatment: 17724097 INFO @ Thu, 16 Apr 2020 05:48:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:48:20: #1 finished! INFO @ Thu, 16 Apr 2020 05:48:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:48:20: 12000000 INFO @ Thu, 16 Apr 2020 05:48:21: #2 number of paired peaks: 519 WARNING @ Thu, 16 Apr 2020 05:48:21: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Thu, 16 Apr 2020 05:48:21: start model_add_line... INFO @ Thu, 16 Apr 2020 05:48:21: start X-correlation... INFO @ Thu, 16 Apr 2020 05:48:21: end of X-cor INFO @ Thu, 16 Apr 2020 05:48:21: #2 finished! INFO @ Thu, 16 Apr 2020 05:48:21: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 05:48:21: #2 alternative fragment length(s) may be 3,78 bps INFO @ Thu, 16 Apr 2020 05:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.10_model.r WARNING @ Thu, 16 Apr 2020 05:48:21: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:48:21: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Thu, 16 Apr 2020 05:48:21: #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 05:48:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:48:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:48:25: 13000000 INFO @ Thu, 16 Apr 2020 05:48:30: 14000000 INFO @ Thu, 16 Apr 2020 05:48:35: 15000000 INFO @ Thu, 16 Apr 2020 05:48:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:48:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:48:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.05_summits.bed INFO @ Thu, 16 Apr 2020 05:48:40: Done! INFO @ Thu, 16 Apr 2020 05:48:41: 16000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3934 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:48:46: 17000000 INFO @ Thu, 16 Apr 2020 05:48:49: #1 tag size is determined as 73 bps INFO @ Thu, 16 Apr 2020 05:48:49: #1 tag size = 73 INFO @ Thu, 16 Apr 2020 05:48:49: #1 total tags in treatment: 17724097 INFO @ Thu, 16 Apr 2020 05:48:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:48:49: #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 05:48:50: #1 tags after filtering in treatment: 17724097 INFO @ Thu, 16 Apr 2020 05:48:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:48:50: #1 finished! INFO @ Thu, 16 Apr 2020 05:48:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:48:51: #2 number of paired peaks: 519 WARNING @ Thu, 16 Apr 2020 05:48:51: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Thu, 16 Apr 2020 05:48:51: start model_add_line... INFO @ Thu, 16 Apr 2020 05:48:51: start X-correlation... INFO @ Thu, 16 Apr 2020 05:48:51: end of X-cor INFO @ Thu, 16 Apr 2020 05:48:51: #2 finished! INFO @ Thu, 16 Apr 2020 05:48:51: #2 predicted fragment length is 78 bps INFO @ Thu, 16 Apr 2020 05:48:51: #2 alternative fragment length(s) may be 3,78 bps INFO @ Thu, 16 Apr 2020 05:48:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.20_model.r WARNING @ Thu, 16 Apr 2020 05:48:51: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:48:51: #2 You may need to consider one of the other alternative d(s): 3,78 WARNING @ Thu, 16 Apr 2020 05:48:51: #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 05:48:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:48:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:49:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:49:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:49:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.10_summits.bed INFO @ Thu, 16 Apr 2020 05:49:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1858 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:49:24: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:49:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:49:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:49:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6747981/SRX6747981.20_summits.bed INFO @ Thu, 16 Apr 2020 05:49:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (780 records, 4 fields): 81 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。