Job ID = 5720697 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:06:45 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 ) 2020-04-15T16:06:45 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 ) 2020-04-15T16:06:45 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 ) 2020-04-15T16:06:45 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 ) 2020-04-15T16:06:45 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 ) 2020-04-15T16:06:45 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 : 22,445,391 reads read : 22,445,391 reads written : 22,445,391 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: 00:05:21 22445391 reads; of these: 22445391 (100.00%) were unpaired; of these: 1348903 (6.01%) aligned 0 times 17685287 (78.79%) aligned exactly 1 time 3411201 (15.20%) aligned >1 times 93.99% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 1913793 / 21096488 = 0.0907 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 01:18:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.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 01:18:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:18:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:18:51: 1000000 INFO @ Thu, 16 Apr 2020 01:18:57: 2000000 INFO @ Thu, 16 Apr 2020 01:19:02: 3000000 INFO @ Thu, 16 Apr 2020 01:19:08: 4000000 INFO @ Thu, 16 Apr 2020 01:19:14: 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 01:19:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.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 01:19:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:19:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:19:19: 6000000 INFO @ Thu, 16 Apr 2020 01:19:21: 1000000 INFO @ Thu, 16 Apr 2020 01:19:25: 7000000 INFO @ Thu, 16 Apr 2020 01:19:27: 2000000 INFO @ Thu, 16 Apr 2020 01:19:31: 8000000 INFO @ Thu, 16 Apr 2020 01:19:33: 3000000 INFO @ Thu, 16 Apr 2020 01:19:37: 9000000 INFO @ Thu, 16 Apr 2020 01:19:39: 4000000 INFO @ Thu, 16 Apr 2020 01:19:43: 10000000 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 01:19:45: 5000000 INFO @ Thu, 16 Apr 2020 01:19:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.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 01:19:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:19:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:19:49: 11000000 INFO @ Thu, 16 Apr 2020 01:19:51: 6000000 INFO @ Thu, 16 Apr 2020 01:19:52: 1000000 INFO @ Thu, 16 Apr 2020 01:19:55: 12000000 INFO @ Thu, 16 Apr 2020 01:19:58: 7000000 INFO @ Thu, 16 Apr 2020 01:19:58: 2000000 INFO @ Thu, 16 Apr 2020 01:20:02: 13000000 INFO @ Thu, 16 Apr 2020 01:20:04: 8000000 INFO @ Thu, 16 Apr 2020 01:20:04: 3000000 INFO @ Thu, 16 Apr 2020 01:20:08: 14000000 INFO @ Thu, 16 Apr 2020 01:20:10: 9000000 INFO @ Thu, 16 Apr 2020 01:20:10: 4000000 INFO @ Thu, 16 Apr 2020 01:20:14: 15000000 INFO @ Thu, 16 Apr 2020 01:20:16: 10000000 INFO @ Thu, 16 Apr 2020 01:20:16: 5000000 INFO @ Thu, 16 Apr 2020 01:20:20: 16000000 INFO @ Thu, 16 Apr 2020 01:20:22: 11000000 INFO @ Thu, 16 Apr 2020 01:20:22: 6000000 INFO @ Thu, 16 Apr 2020 01:20:26: 17000000 INFO @ Thu, 16 Apr 2020 01:20:28: 12000000 INFO @ Thu, 16 Apr 2020 01:20:28: 7000000 INFO @ Thu, 16 Apr 2020 01:20:32: 18000000 INFO @ Thu, 16 Apr 2020 01:20:34: 13000000 INFO @ Thu, 16 Apr 2020 01:20:35: 8000000 INFO @ Thu, 16 Apr 2020 01:20:38: 19000000 INFO @ Thu, 16 Apr 2020 01:20:39: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:20:39: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:20:39: #1 total tags in treatment: 19182695 INFO @ Thu, 16 Apr 2020 01:20:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:20:39: #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 01:20:40: #1 tags after filtering in treatment: 19182695 INFO @ Thu, 16 Apr 2020 01:20:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:20:40: #1 finished! INFO @ Thu, 16 Apr 2020 01:20:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:20:41: 9000000 INFO @ Thu, 16 Apr 2020 01:20:41: 14000000 INFO @ Thu, 16 Apr 2020 01:20:41: #2 number of paired peaks: 105 WARNING @ Thu, 16 Apr 2020 01:20:41: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Thu, 16 Apr 2020 01:20:41: start model_add_line... INFO @ Thu, 16 Apr 2020 01:20:41: start X-correlation... INFO @ Thu, 16 Apr 2020 01:20:41: end of X-cor INFO @ Thu, 16 Apr 2020 01:20:41: #2 finished! INFO @ Thu, 16 Apr 2020 01:20:41: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 01:20:41: #2 alternative fragment length(s) may be 2,47,126,197,292,385,477,564,597 bps INFO @ Thu, 16 Apr 2020 01:20:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.05_model.r WARNING @ Thu, 16 Apr 2020 01:20:41: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:20:41: #2 You may need to consider one of the other alternative d(s): 2,47,126,197,292,385,477,564,597 WARNING @ Thu, 16 Apr 2020 01:20:41: #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 01:20:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:20:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:20:47: 15000000 INFO @ Thu, 16 Apr 2020 01:20:47: 10000000 INFO @ Thu, 16 Apr 2020 01:20:53: 11000000 INFO @ Thu, 16 Apr 2020 01:20:53: 16000000 INFO @ Thu, 16 Apr 2020 01:20:59: 12000000 INFO @ Thu, 16 Apr 2020 01:20:59: 17000000 INFO @ Thu, 16 Apr 2020 01:21:05: 13000000 INFO @ Thu, 16 Apr 2020 01:21:05: 18000000 INFO @ Thu, 16 Apr 2020 01:21:11: 14000000 INFO @ Thu, 16 Apr 2020 01:21:11: 19000000 INFO @ Thu, 16 Apr 2020 01:21:12: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:21:12: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:21:12: #1 total tags in treatment: 19182695 INFO @ Thu, 16 Apr 2020 01:21:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:12: #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 01:21:13: #1 tags after filtering in treatment: 19182695 INFO @ Thu, 16 Apr 2020 01:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:13: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:14: #2 number of paired peaks: 105 WARNING @ Thu, 16 Apr 2020 01:21:14: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Thu, 16 Apr 2020 01:21:14: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:14: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:14: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:14: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:14: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 01:21:14: #2 alternative fragment length(s) may be 2,47,126,197,292,385,477,564,597 bps INFO @ Thu, 16 Apr 2020 01:21:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.10_model.r WARNING @ Thu, 16 Apr 2020 01:21:14: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:14: #2 You may need to consider one of the other alternative d(s): 2,47,126,197,292,385,477,564,597 WARNING @ Thu, 16 Apr 2020 01:21:14: #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 01:21:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:17: 15000000 INFO @ Thu, 16 Apr 2020 01:21:22: 16000000 INFO @ Thu, 16 Apr 2020 01:21:28: 17000000 INFO @ Thu, 16 Apr 2020 01:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.05_summits.bed INFO @ Thu, 16 Apr 2020 01:21:34: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:21:34: 18000000 INFO @ Thu, 16 Apr 2020 01:21:40: 19000000 INFO @ Thu, 16 Apr 2020 01:21:41: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:21:41: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:21:41: #1 total tags in treatment: 19182695 INFO @ Thu, 16 Apr 2020 01:21:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:41: #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 01:21:41: #1 tags after filtering in treatment: 19182695 INFO @ Thu, 16 Apr 2020 01:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:41: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:42: #2 number of paired peaks: 105 WARNING @ Thu, 16 Apr 2020 01:21:42: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Thu, 16 Apr 2020 01:21:42: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:42: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:43: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:43: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:43: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 01:21:43: #2 alternative fragment length(s) may be 2,47,126,197,292,385,477,564,597 bps INFO @ Thu, 16 Apr 2020 01:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.20_model.r WARNING @ Thu, 16 Apr 2020 01:21:43: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:43: #2 You may need to consider one of the other alternative d(s): 2,47,126,197,292,385,477,564,597 WARNING @ Thu, 16 Apr 2020 01:21:43: #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 01:21:43: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:22:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:22:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:22:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.10_summits.bed INFO @ Thu, 16 Apr 2020 01:22:07: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:22:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:22:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:22:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:22:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158162/SRX4158162.20_summits.bed INFO @ Thu, 16 Apr 2020 01:22:36: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。