Job ID = 5720917 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:15:07 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 ) 2020-04-15T18:15:07 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 ) 2020-04-15T18:15:07 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 ) 2020-04-15T18:15:07 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 ) 2020-04-15T18:15:07 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 ) 2020-04-15T18:15:07 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 : 29,321,608 reads read : 58,643,216 reads written : 29,321,608 reads 0-length : 29,321,608 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:58 29321608 reads; of these: 29321608 (100.00%) were unpaired; of these: 896681 (3.06%) aligned 0 times 19540975 (66.64%) aligned exactly 1 time 8883952 (30.30%) aligned >1 times 96.94% overall alignment rate Time searching: 00:11:59 Overall time: 00:11:59 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] 11857702 / 28424927 = 0.4172 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 03:42:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.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 03:42:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:42:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:42:14: 1000000 INFO @ Thu, 16 Apr 2020 03:42:20: 2000000 INFO @ Thu, 16 Apr 2020 03:42:26: 3000000 INFO @ Thu, 16 Apr 2020 03:42:33: 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 03:42:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.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 03:42:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:42:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:42:39: 5000000 INFO @ Thu, 16 Apr 2020 03:42:45: 1000000 INFO @ Thu, 16 Apr 2020 03:42:46: 6000000 INFO @ Thu, 16 Apr 2020 03:42:52: 2000000 INFO @ Thu, 16 Apr 2020 03:42:52: 7000000 INFO @ Thu, 16 Apr 2020 03:42:59: 3000000 INFO @ Thu, 16 Apr 2020 03:42:59: 8000000 INFO @ Thu, 16 Apr 2020 03:43:06: 4000000 INFO @ Thu, 16 Apr 2020 03:43:06: 9000000 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 03:43:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.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 03:43:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:43:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:43:12: 5000000 INFO @ Thu, 16 Apr 2020 03:43:13: 10000000 INFO @ Thu, 16 Apr 2020 03:43:15: 1000000 INFO @ Thu, 16 Apr 2020 03:43:20: 6000000 INFO @ Thu, 16 Apr 2020 03:43:20: 11000000 INFO @ Thu, 16 Apr 2020 03:43:22: 2000000 INFO @ Thu, 16 Apr 2020 03:43:26: 7000000 INFO @ Thu, 16 Apr 2020 03:43:27: 12000000 INFO @ Thu, 16 Apr 2020 03:43:29: 3000000 INFO @ Thu, 16 Apr 2020 03:43:34: 8000000 INFO @ Thu, 16 Apr 2020 03:43:34: 13000000 INFO @ Thu, 16 Apr 2020 03:43:36: 4000000 INFO @ Thu, 16 Apr 2020 03:43:40: 9000000 INFO @ Thu, 16 Apr 2020 03:43:41: 14000000 INFO @ Thu, 16 Apr 2020 03:43:43: 5000000 INFO @ Thu, 16 Apr 2020 03:43:48: 10000000 INFO @ Thu, 16 Apr 2020 03:43:48: 15000000 INFO @ Thu, 16 Apr 2020 03:43:50: 6000000 INFO @ Thu, 16 Apr 2020 03:43:55: 11000000 INFO @ Thu, 16 Apr 2020 03:43:55: 16000000 INFO @ Thu, 16 Apr 2020 03:43:57: 7000000 INFO @ Thu, 16 Apr 2020 03:44:00: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 03:44:00: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 03:44:00: #1 total tags in treatment: 16567225 INFO @ Thu, 16 Apr 2020 03:44:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:44:00: #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 03:44:00: #1 tags after filtering in treatment: 16567225 INFO @ Thu, 16 Apr 2020 03:44:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:44:00: #1 finished! INFO @ Thu, 16 Apr 2020 03:44:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:44:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:44:01: #2 number of paired peaks: 117 WARNING @ Thu, 16 Apr 2020 03:44:01: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Thu, 16 Apr 2020 03:44:01: start model_add_line... INFO @ Thu, 16 Apr 2020 03:44:01: start X-correlation... INFO @ Thu, 16 Apr 2020 03:44:01: end of X-cor INFO @ Thu, 16 Apr 2020 03:44:01: #2 finished! INFO @ Thu, 16 Apr 2020 03:44:01: #2 predicted fragment length is 71 bps INFO @ Thu, 16 Apr 2020 03:44:01: #2 alternative fragment length(s) may be 4,71,562,564 bps INFO @ Thu, 16 Apr 2020 03:44:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.05_model.r WARNING @ Thu, 16 Apr 2020 03:44:01: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:44:01: #2 You may need to consider one of the other alternative d(s): 4,71,562,564 WARNING @ Thu, 16 Apr 2020 03:44:01: #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 03:44:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:44:02: 12000000 INFO @ Thu, 16 Apr 2020 03:44:04: 8000000 INFO @ Thu, 16 Apr 2020 03:44:09: 13000000 INFO @ Thu, 16 Apr 2020 03:44:11: 9000000 INFO @ Thu, 16 Apr 2020 03:44:16: 14000000 INFO @ Thu, 16 Apr 2020 03:44:18: 10000000 INFO @ Thu, 16 Apr 2020 03:44:23: 15000000 INFO @ Thu, 16 Apr 2020 03:44:25: 11000000 INFO @ Thu, 16 Apr 2020 03:44:30: 16000000 INFO @ Thu, 16 Apr 2020 03:44:33: 12000000 INFO @ Thu, 16 Apr 2020 03:44:35: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 03:44:35: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 03:44:35: #1 total tags in treatment: 16567225 INFO @ Thu, 16 Apr 2020 03:44:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:44:35: #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 03:44:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:44:35: #1 tags after filtering in treatment: 16567225 INFO @ Thu, 16 Apr 2020 03:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:44:35: #1 finished! INFO @ Thu, 16 Apr 2020 03:44:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:44:36: #2 number of paired peaks: 117 WARNING @ Thu, 16 Apr 2020 03:44:36: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Thu, 16 Apr 2020 03:44:36: start model_add_line... INFO @ Thu, 16 Apr 2020 03:44:36: start X-correlation... INFO @ Thu, 16 Apr 2020 03:44:36: end of X-cor INFO @ Thu, 16 Apr 2020 03:44:36: #2 finished! INFO @ Thu, 16 Apr 2020 03:44:36: #2 predicted fragment length is 71 bps INFO @ Thu, 16 Apr 2020 03:44:36: #2 alternative fragment length(s) may be 4,71,562,564 bps INFO @ Thu, 16 Apr 2020 03:44:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.10_model.r WARNING @ Thu, 16 Apr 2020 03:44:36: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:44:36: #2 You may need to consider one of the other alternative d(s): 4,71,562,564 WARNING @ Thu, 16 Apr 2020 03:44:36: #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 03:44:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:44:39: 13000000 INFO @ Thu, 16 Apr 2020 03:44:46: 14000000 INFO @ Thu, 16 Apr 2020 03:44:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:44:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:44:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.05_summits.bed INFO @ Thu, 16 Apr 2020 03:44:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2408 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:44:52: 15000000 INFO @ Thu, 16 Apr 2020 03:44:59: 16000000 INFO @ Thu, 16 Apr 2020 03:45:02: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 03:45:02: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 03:45:02: #1 total tags in treatment: 16567225 INFO @ Thu, 16 Apr 2020 03:45:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:45:02: #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 03:45:03: #1 tags after filtering in treatment: 16567225 INFO @ Thu, 16 Apr 2020 03:45:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:45:03: #1 finished! INFO @ Thu, 16 Apr 2020 03:45:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:45:04: #2 number of paired peaks: 117 WARNING @ Thu, 16 Apr 2020 03:45:04: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Thu, 16 Apr 2020 03:45:04: start model_add_line... INFO @ Thu, 16 Apr 2020 03:45:04: start X-correlation... INFO @ Thu, 16 Apr 2020 03:45:04: end of X-cor INFO @ Thu, 16 Apr 2020 03:45:04: #2 finished! INFO @ Thu, 16 Apr 2020 03:45:04: #2 predicted fragment length is 71 bps INFO @ Thu, 16 Apr 2020 03:45:04: #2 alternative fragment length(s) may be 4,71,562,564 bps INFO @ Thu, 16 Apr 2020 03:45:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.20_model.r WARNING @ Thu, 16 Apr 2020 03:45:04: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:45:04: #2 You may need to consider one of the other alternative d(s): 4,71,562,564 WARNING @ Thu, 16 Apr 2020 03:45:04: #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 03:45:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:45:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:45:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.10_summits.bed INFO @ Thu, 16 Apr 2020 03:45:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1155 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:45:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:45:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:45:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:45:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775944/SRX5775944.20_summits.bed INFO @ Thu, 16 Apr 2020 03:45:53: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (521 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。