Job ID = 5720733 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T16:05:24 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 ) 2020-04-15T16:05:24 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 ) 2020-04-15T16:05:24 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 ) 2020-04-15T16:05:24 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 ) 2020-04-15T16:05:24 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 : 13,605,321 reads read : 27,210,642 reads written : 13,605,321 reads 0-length : 13,605,321 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: 00:05:27 13605321 reads; of these: 13605321 (100.00%) were unpaired; of these: 1006197 (7.40%) aligned 0 times 9240891 (67.92%) aligned exactly 1 time 3358233 (24.68%) aligned >1 times 92.60% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 1055304 / 12599124 = 0.0838 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 01:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.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 01:19:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:19:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:19:50: 1000000 INFO @ Thu, 16 Apr 2020 01:19:55: 2000000 INFO @ Thu, 16 Apr 2020 01:20:01: 3000000 INFO @ Thu, 16 Apr 2020 01:20:06: 4000000 INFO @ Thu, 16 Apr 2020 01:20:11: 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 01:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.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 01:20:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:20:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:20:17: 6000000 INFO @ Thu, 16 Apr 2020 01:20:20: 1000000 INFO @ Thu, 16 Apr 2020 01:20:23: 7000000 INFO @ Thu, 16 Apr 2020 01:20:26: 2000000 INFO @ Thu, 16 Apr 2020 01:20:29: 8000000 INFO @ Thu, 16 Apr 2020 01:20:32: 3000000 INFO @ Thu, 16 Apr 2020 01:20:35: 9000000 INFO @ Thu, 16 Apr 2020 01:20:38: 4000000 INFO @ Thu, 16 Apr 2020 01:20:41: 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 01:20:44: 5000000 INFO @ Thu, 16 Apr 2020 01:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.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 01:20:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:20:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:20:47: 11000000 INFO @ Thu, 16 Apr 2020 01:20:50: 6000000 INFO @ Thu, 16 Apr 2020 01:20:51: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:20:51: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:20:51: #1 total tags in treatment: 11543820 INFO @ Thu, 16 Apr 2020 01:20:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:20:51: #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 01:20:51: #1 tags after filtering in treatment: 11543820 INFO @ Thu, 16 Apr 2020 01:20:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:20:51: #1 finished! INFO @ Thu, 16 Apr 2020 01:20:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:20:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:20:51: 1000000 INFO @ Thu, 16 Apr 2020 01:20:52: #2 number of paired peaks: 667 WARNING @ Thu, 16 Apr 2020 01:20:52: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Thu, 16 Apr 2020 01:20:52: start model_add_line... INFO @ Thu, 16 Apr 2020 01:20:52: start X-correlation... INFO @ Thu, 16 Apr 2020 01:20:52: end of X-cor INFO @ Thu, 16 Apr 2020 01:20:52: #2 finished! INFO @ Thu, 16 Apr 2020 01:20:52: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 01:20:52: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 01:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.05_model.r WARNING @ Thu, 16 Apr 2020 01:20:52: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:20:52: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 01:20:52: #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 01:20:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:20:57: 7000000 INFO @ Thu, 16 Apr 2020 01:20:59: 2000000 INFO @ Thu, 16 Apr 2020 01:21:03: 8000000 INFO @ Thu, 16 Apr 2020 01:21:06: 3000000 INFO @ Thu, 16 Apr 2020 01:21:09: 9000000 INFO @ Thu, 16 Apr 2020 01:21:13: 4000000 INFO @ Thu, 16 Apr 2020 01:21:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:15: 10000000 INFO @ Thu, 16 Apr 2020 01:21:20: 5000000 INFO @ Thu, 16 Apr 2020 01:21:21: 11000000 INFO @ Thu, 16 Apr 2020 01:21:24: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:21:24: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:21:24: #1 total tags in treatment: 11543820 INFO @ Thu, 16 Apr 2020 01:21:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:21:24: #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 01:21:25: #1 tags after filtering in treatment: 11543820 INFO @ Thu, 16 Apr 2020 01:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:21:25: #1 finished! INFO @ Thu, 16 Apr 2020 01:21:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:21:25: #2 number of paired peaks: 667 WARNING @ Thu, 16 Apr 2020 01:21:25: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Thu, 16 Apr 2020 01:21:25: start model_add_line... INFO @ Thu, 16 Apr 2020 01:21:26: start X-correlation... INFO @ Thu, 16 Apr 2020 01:21:26: end of X-cor INFO @ Thu, 16 Apr 2020 01:21:26: #2 finished! INFO @ Thu, 16 Apr 2020 01:21:26: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 01:21:26: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 01:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.10_model.r WARNING @ Thu, 16 Apr 2020 01:21:26: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:21:26: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 01:21:26: #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 01:21:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:21:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:21:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.05_summits.bed INFO @ Thu, 16 Apr 2020 01:21:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4180 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:21:27: 6000000 INFO @ Thu, 16 Apr 2020 01:21:33: 7000000 INFO @ Thu, 16 Apr 2020 01:21:40: 8000000 INFO @ Thu, 16 Apr 2020 01:21:47: 9000000 INFO @ Thu, 16 Apr 2020 01:21:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:21:53: 10000000 INFO @ Thu, 16 Apr 2020 01:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.10_summits.bed INFO @ Thu, 16 Apr 2020 01:21:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1937 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:22:00: 11000000 INFO @ Thu, 16 Apr 2020 01:22:03: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:22:03: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:22:03: #1 total tags in treatment: 11543820 INFO @ Thu, 16 Apr 2020 01:22:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:22:03: #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 01:22:04: #1 tags after filtering in treatment: 11543820 INFO @ Thu, 16 Apr 2020 01:22:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:22:04: #1 finished! INFO @ Thu, 16 Apr 2020 01:22:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:22:04: #2 number of paired peaks: 667 WARNING @ Thu, 16 Apr 2020 01:22:04: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Thu, 16 Apr 2020 01:22:04: start model_add_line... INFO @ Thu, 16 Apr 2020 01:22:04: start X-correlation... INFO @ Thu, 16 Apr 2020 01:22:04: end of X-cor INFO @ Thu, 16 Apr 2020 01:22:04: #2 finished! INFO @ Thu, 16 Apr 2020 01:22:04: #2 predicted fragment length is 80 bps INFO @ Thu, 16 Apr 2020 01:22:04: #2 alternative fragment length(s) may be 80 bps INFO @ Thu, 16 Apr 2020 01:22:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.20_model.r WARNING @ Thu, 16 Apr 2020 01:22:04: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:22:04: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Thu, 16 Apr 2020 01:22:04: #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 01:22:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:22:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:22:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:22:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:22:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:22:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5226972/SRX5226972.20_summits.bed INFO @ Thu, 16 Apr 2020 01:22:38: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (717 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。