Job ID = 5720863 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:27:40 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 ) 2020-04-15T17:27:40 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 ) 2020-04-15T17:27:40 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 : 46,698,560 reads read : 46,698,560 reads written : 46,698,560 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: 00:11:32 46698560 reads; of these: 46698560 (100.00%) were unpaired; of these: 11136241 (23.85%) aligned 0 times 25772055 (55.19%) aligned exactly 1 time 9790264 (20.96%) aligned >1 times 76.15% overall alignment rate Time searching: 00:11:32 Overall time: 00:11:32 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 16 files... [bam_rmdupse_core] 12547147 / 35562319 = 0.3528 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 02:56:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.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 02:56:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:56:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:57:00: 1000000 INFO @ Thu, 16 Apr 2020 02:57:05: 2000000 INFO @ Thu, 16 Apr 2020 02:57:11: 3000000 INFO @ Thu, 16 Apr 2020 02:57:16: 4000000 INFO @ Thu, 16 Apr 2020 02:57:21: 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 02:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.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 02:57:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:57:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:57:26: 6000000 INFO @ Thu, 16 Apr 2020 02:57:31: 1000000 INFO @ Thu, 16 Apr 2020 02:57:32: 7000000 INFO @ Thu, 16 Apr 2020 02:57:37: 2000000 INFO @ Thu, 16 Apr 2020 02:57:38: 8000000 INFO @ Thu, 16 Apr 2020 02:57:43: 3000000 INFO @ Thu, 16 Apr 2020 02:57:43: 9000000 INFO @ Thu, 16 Apr 2020 02:57:48: 4000000 INFO @ Thu, 16 Apr 2020 02:57:49: 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 02:57:54: 5000000 INFO @ Thu, 16 Apr 2020 02:57:54: 11000000 INFO @ Thu, 16 Apr 2020 02:57:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.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 02:57:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:57:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:58:00: 6000000 INFO @ Thu, 16 Apr 2020 02:58:00: 12000000 INFO @ Thu, 16 Apr 2020 02:58:02: 1000000 INFO @ Thu, 16 Apr 2020 02:58:06: 7000000 INFO @ Thu, 16 Apr 2020 02:58:06: 13000000 INFO @ Thu, 16 Apr 2020 02:58:09: 2000000 INFO @ Thu, 16 Apr 2020 02:58:12: 8000000 INFO @ Thu, 16 Apr 2020 02:58:12: 14000000 INFO @ Thu, 16 Apr 2020 02:58:16: 3000000 INFO @ Thu, 16 Apr 2020 02:58:18: 9000000 INFO @ Thu, 16 Apr 2020 02:58:19: 15000000 INFO @ Thu, 16 Apr 2020 02:58:22: 4000000 INFO @ Thu, 16 Apr 2020 02:58:25: 10000000 INFO @ Thu, 16 Apr 2020 02:58:25: 16000000 INFO @ Thu, 16 Apr 2020 02:58:29: 5000000 INFO @ Thu, 16 Apr 2020 02:58:31: 17000000 INFO @ Thu, 16 Apr 2020 02:58:31: 11000000 INFO @ Thu, 16 Apr 2020 02:58:35: 6000000 INFO @ Thu, 16 Apr 2020 02:58:37: 12000000 INFO @ Thu, 16 Apr 2020 02:58:37: 18000000 INFO @ Thu, 16 Apr 2020 02:58:42: 7000000 INFO @ Thu, 16 Apr 2020 02:58:43: 13000000 INFO @ Thu, 16 Apr 2020 02:58:43: 19000000 INFO @ Thu, 16 Apr 2020 02:58:49: 8000000 INFO @ Thu, 16 Apr 2020 02:58:49: 14000000 INFO @ Thu, 16 Apr 2020 02:58:49: 20000000 INFO @ Thu, 16 Apr 2020 02:58:55: 15000000 INFO @ Thu, 16 Apr 2020 02:58:55: 9000000 INFO @ Thu, 16 Apr 2020 02:58:55: 21000000 INFO @ Thu, 16 Apr 2020 02:59:01: 16000000 INFO @ Thu, 16 Apr 2020 02:59:02: 22000000 INFO @ Thu, 16 Apr 2020 02:59:02: 10000000 INFO @ Thu, 16 Apr 2020 02:59:08: 23000000 INFO @ Thu, 16 Apr 2020 02:59:08: 17000000 INFO @ Thu, 16 Apr 2020 02:59:08: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:59:08: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:59:08: #1 total tags in treatment: 23015172 INFO @ Thu, 16 Apr 2020 02:59:08: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:59:08: #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 02:59:08: #1 tags after filtering in treatment: 23015172 INFO @ Thu, 16 Apr 2020 02:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:59:08: #1 finished! INFO @ Thu, 16 Apr 2020 02:59:08: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:59:09: 11000000 INFO @ Thu, 16 Apr 2020 02:59:10: #2 number of paired peaks: 640 WARNING @ Thu, 16 Apr 2020 02:59:10: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Thu, 16 Apr 2020 02:59:10: start model_add_line... INFO @ Thu, 16 Apr 2020 02:59:10: start X-correlation... INFO @ Thu, 16 Apr 2020 02:59:10: end of X-cor INFO @ Thu, 16 Apr 2020 02:59:10: #2 finished! INFO @ Thu, 16 Apr 2020 02:59:10: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 02:59:10: #2 alternative fragment length(s) may be 3,51 bps INFO @ Thu, 16 Apr 2020 02:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.05_model.r WARNING @ Thu, 16 Apr 2020 02:59:10: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:59:10: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Thu, 16 Apr 2020 02:59:10: #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 02:59:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:59:14: 18000000 INFO @ Thu, 16 Apr 2020 02:59:15: 12000000 INFO @ Thu, 16 Apr 2020 02:59:20: 19000000 INFO @ Thu, 16 Apr 2020 02:59:22: 13000000 INFO @ Thu, 16 Apr 2020 02:59:26: 20000000 INFO @ Thu, 16 Apr 2020 02:59:28: 14000000 INFO @ Thu, 16 Apr 2020 02:59:32: 21000000 INFO @ Thu, 16 Apr 2020 02:59:35: 15000000 INFO @ Thu, 16 Apr 2020 02:59:38: 22000000 INFO @ Thu, 16 Apr 2020 02:59:41: 16000000 INFO @ Thu, 16 Apr 2020 02:59:44: 23000000 INFO @ Thu, 16 Apr 2020 02:59:44: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:59:44: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:59:44: #1 total tags in treatment: 23015172 INFO @ Thu, 16 Apr 2020 02:59:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:59:44: #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 02:59:45: #1 tags after filtering in treatment: 23015172 INFO @ Thu, 16 Apr 2020 02:59:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:59:45: #1 finished! INFO @ Thu, 16 Apr 2020 02:59:45: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:59:46: #2 number of paired peaks: 640 WARNING @ Thu, 16 Apr 2020 02:59:46: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Thu, 16 Apr 2020 02:59:46: start model_add_line... INFO @ Thu, 16 Apr 2020 02:59:46: start X-correlation... INFO @ Thu, 16 Apr 2020 02:59:47: end of X-cor INFO @ Thu, 16 Apr 2020 02:59:47: #2 finished! INFO @ Thu, 16 Apr 2020 02:59:47: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 02:59:47: #2 alternative fragment length(s) may be 3,51 bps INFO @ Thu, 16 Apr 2020 02:59:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.10_model.r WARNING @ Thu, 16 Apr 2020 02:59:47: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:59:47: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Thu, 16 Apr 2020 02:59:47: #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 02:59:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:59:48: 17000000 INFO @ Thu, 16 Apr 2020 02:59:52: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:59:54: 18000000 INFO @ Thu, 16 Apr 2020 03:00:00: 19000000 INFO @ Thu, 16 Apr 2020 03:00:06: 20000000 INFO @ Thu, 16 Apr 2020 03:00:13: 21000000 INFO @ Thu, 16 Apr 2020 03:00:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:00:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:00:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.05_summits.bed INFO @ Thu, 16 Apr 2020 03:00:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5899 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:00:19: 22000000 INFO @ Thu, 16 Apr 2020 03:00:25: 23000000 INFO @ Thu, 16 Apr 2020 03:00:25: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 03:00:25: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 03:00:25: #1 total tags in treatment: 23015172 INFO @ Thu, 16 Apr 2020 03:00:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:00:25: #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 03:00:25: #1 tags after filtering in treatment: 23015172 INFO @ Thu, 16 Apr 2020 03:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:00:25: #1 finished! INFO @ Thu, 16 Apr 2020 03:00:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:00:27: #2 number of paired peaks: 640 WARNING @ Thu, 16 Apr 2020 03:00:27: Fewer paired peaks (640) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 640 pairs to build model! INFO @ Thu, 16 Apr 2020 03:00:27: start model_add_line... INFO @ Thu, 16 Apr 2020 03:00:27: start X-correlation... INFO @ Thu, 16 Apr 2020 03:00:27: end of X-cor INFO @ Thu, 16 Apr 2020 03:00:27: #2 finished! INFO @ Thu, 16 Apr 2020 03:00:27: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 03:00:27: #2 alternative fragment length(s) may be 3,51 bps INFO @ Thu, 16 Apr 2020 03:00:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.20_model.r WARNING @ Thu, 16 Apr 2020 03:00:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:00:27: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Thu, 16 Apr 2020 03:00:27: #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 03:00:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:00:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:00:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.10_summits.bed INFO @ Thu, 16 Apr 2020 03:00:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3219 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:01:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:01:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:01:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:01:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436052/SRX5436052.20_summits.bed INFO @ Thu, 16 Apr 2020 03:01:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1435 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。