Job ID = 5720861 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:17:27 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 ) 2020-04-15T17:17:27 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 : 34,862,720 reads read : 34,862,720 reads written : 34,862,720 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: 00:11:39 34862720 reads; of these: 34862720 (100.00%) were unpaired; of these: 923361 (2.65%) aligned 0 times 22730145 (65.20%) aligned exactly 1 time 11209214 (32.15%) aligned >1 times 97.35% overall alignment rate Time searching: 00:11:39 Overall time: 00:11:39 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] 5547008 / 33939359 = 0.1634 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 02:51:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.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 02:51:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:51:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:51:22: 1000000 INFO @ Thu, 16 Apr 2020 02:51:27: 2000000 INFO @ Thu, 16 Apr 2020 02:51:31: 3000000 INFO @ Thu, 16 Apr 2020 02:51:36: 4000000 INFO @ Thu, 16 Apr 2020 02:51:41: 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 02:51:45: 6000000 INFO @ Thu, 16 Apr 2020 02:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.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 02:51:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:51:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:51:50: 7000000 INFO @ Thu, 16 Apr 2020 02:51:53: 1000000 INFO @ Thu, 16 Apr 2020 02:51:55: 8000000 INFO @ Thu, 16 Apr 2020 02:51:57: 2000000 INFO @ Thu, 16 Apr 2020 02:51:59: 9000000 INFO @ Thu, 16 Apr 2020 02:52:03: 3000000 INFO @ Thu, 16 Apr 2020 02:52:04: 10000000 INFO @ Thu, 16 Apr 2020 02:52:07: 4000000 INFO @ Thu, 16 Apr 2020 02:52:09: 11000000 INFO @ Thu, 16 Apr 2020 02:52:13: 12000000 INFO @ Thu, 16 Apr 2020 02:52:14: 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 02:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.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 02:52:17: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:52:17: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:52:18: 13000000 INFO @ Thu, 16 Apr 2020 02:52:18: 6000000 INFO @ Thu, 16 Apr 2020 02:52:22: 1000000 INFO @ Thu, 16 Apr 2020 02:52:23: 14000000 INFO @ Thu, 16 Apr 2020 02:52:23: 7000000 INFO @ Thu, 16 Apr 2020 02:52:27: 2000000 INFO @ Thu, 16 Apr 2020 02:52:28: 15000000 INFO @ Thu, 16 Apr 2020 02:52:28: 8000000 INFO @ Thu, 16 Apr 2020 02:52:32: 3000000 INFO @ Thu, 16 Apr 2020 02:52:32: 16000000 INFO @ Thu, 16 Apr 2020 02:52:33: 9000000 INFO @ Thu, 16 Apr 2020 02:52:37: 4000000 INFO @ Thu, 16 Apr 2020 02:52:37: 17000000 INFO @ Thu, 16 Apr 2020 02:52:37: 10000000 INFO @ Thu, 16 Apr 2020 02:52:42: 5000000 INFO @ Thu, 16 Apr 2020 02:52:42: 18000000 INFO @ Thu, 16 Apr 2020 02:52:42: 11000000 INFO @ Thu, 16 Apr 2020 02:52:46: 6000000 INFO @ Thu, 16 Apr 2020 02:52:47: 12000000 INFO @ Thu, 16 Apr 2020 02:52:47: 19000000 INFO @ Thu, 16 Apr 2020 02:52:51: 7000000 INFO @ Thu, 16 Apr 2020 02:52:51: 13000000 INFO @ Thu, 16 Apr 2020 02:52:51: 20000000 INFO @ Thu, 16 Apr 2020 02:52:56: 8000000 INFO @ Thu, 16 Apr 2020 02:52:56: 14000000 INFO @ Thu, 16 Apr 2020 02:52:56: 21000000 INFO @ Thu, 16 Apr 2020 02:53:01: 9000000 INFO @ Thu, 16 Apr 2020 02:53:01: 22000000 INFO @ Thu, 16 Apr 2020 02:53:02: 15000000 INFO @ Thu, 16 Apr 2020 02:53:05: 10000000 INFO @ Thu, 16 Apr 2020 02:53:06: 23000000 INFO @ Thu, 16 Apr 2020 02:53:07: 16000000 INFO @ Thu, 16 Apr 2020 02:53:10: 11000000 INFO @ Thu, 16 Apr 2020 02:53:11: 24000000 INFO @ Thu, 16 Apr 2020 02:53:11: 17000000 INFO @ Thu, 16 Apr 2020 02:53:15: 12000000 INFO @ Thu, 16 Apr 2020 02:53:16: 25000000 INFO @ Thu, 16 Apr 2020 02:53:16: 18000000 INFO @ Thu, 16 Apr 2020 02:53:20: 13000000 INFO @ Thu, 16 Apr 2020 02:53:21: 19000000 INFO @ Thu, 16 Apr 2020 02:53:21: 26000000 INFO @ Thu, 16 Apr 2020 02:53:24: 14000000 INFO @ Thu, 16 Apr 2020 02:53:26: 20000000 INFO @ Thu, 16 Apr 2020 02:53:26: 27000000 INFO @ Thu, 16 Apr 2020 02:53:29: 15000000 INFO @ Thu, 16 Apr 2020 02:53:30: 21000000 INFO @ Thu, 16 Apr 2020 02:53:31: 28000000 INFO @ Thu, 16 Apr 2020 02:53:33: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:53:33: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:53:33: #1 total tags in treatment: 28392351 INFO @ Thu, 16 Apr 2020 02:53:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:53:33: #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 02:53:33: #1 tags after filtering in treatment: 28392351 INFO @ Thu, 16 Apr 2020 02:53:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:53:33: #1 finished! INFO @ Thu, 16 Apr 2020 02:53:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:53:34: 16000000 INFO @ Thu, 16 Apr 2020 02:53:35: 22000000 INFO @ Thu, 16 Apr 2020 02:53:35: #2 number of paired peaks: 447 WARNING @ Thu, 16 Apr 2020 02:53:35: Fewer paired peaks (447) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 447 pairs to build model! INFO @ Thu, 16 Apr 2020 02:53:35: start model_add_line... INFO @ Thu, 16 Apr 2020 02:53:35: start X-correlation... INFO @ Thu, 16 Apr 2020 02:53:35: end of X-cor INFO @ Thu, 16 Apr 2020 02:53:35: #2 finished! INFO @ Thu, 16 Apr 2020 02:53:35: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:53:35: #2 alternative fragment length(s) may be 1,43,559,562 bps INFO @ Thu, 16 Apr 2020 02:53:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.05_model.r WARNING @ Thu, 16 Apr 2020 02:53:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:53:35: #2 You may need to consider one of the other alternative d(s): 1,43,559,562 WARNING @ Thu, 16 Apr 2020 02:53:35: #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 02:53:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:53:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:53:38: 17000000 INFO @ Thu, 16 Apr 2020 02:53:40: 23000000 INFO @ Thu, 16 Apr 2020 02:53:43: 18000000 INFO @ Thu, 16 Apr 2020 02:53:44: 24000000 INFO @ Thu, 16 Apr 2020 02:53:48: 19000000 INFO @ Thu, 16 Apr 2020 02:53:49: 25000000 INFO @ Thu, 16 Apr 2020 02:53:52: 20000000 INFO @ Thu, 16 Apr 2020 02:53:54: 26000000 INFO @ Thu, 16 Apr 2020 02:53:57: 21000000 INFO @ Thu, 16 Apr 2020 02:53:58: 27000000 INFO @ Thu, 16 Apr 2020 02:54:01: 22000000 INFO @ Thu, 16 Apr 2020 02:54:03: 28000000 INFO @ Thu, 16 Apr 2020 02:54:05: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:54:05: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:54:05: #1 total tags in treatment: 28392351 INFO @ Thu, 16 Apr 2020 02:54:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:54:05: #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 02:54:06: #1 tags after filtering in treatment: 28392351 INFO @ Thu, 16 Apr 2020 02:54:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:54:06: #1 finished! INFO @ Thu, 16 Apr 2020 02:54:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:54:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:54:06: 23000000 INFO @ Thu, 16 Apr 2020 02:54:08: #2 number of paired peaks: 447 WARNING @ Thu, 16 Apr 2020 02:54:08: Fewer paired peaks (447) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 447 pairs to build model! INFO @ Thu, 16 Apr 2020 02:54:08: start model_add_line... INFO @ Thu, 16 Apr 2020 02:54:08: start X-correlation... INFO @ Thu, 16 Apr 2020 02:54:08: end of X-cor INFO @ Thu, 16 Apr 2020 02:54:08: #2 finished! INFO @ Thu, 16 Apr 2020 02:54:08: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:54:08: #2 alternative fragment length(s) may be 1,43,559,562 bps INFO @ Thu, 16 Apr 2020 02:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.10_model.r WARNING @ Thu, 16 Apr 2020 02:54:08: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:54:08: #2 You may need to consider one of the other alternative d(s): 1,43,559,562 WARNING @ Thu, 16 Apr 2020 02:54:08: #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 02:54:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:54:11: 24000000 INFO @ Thu, 16 Apr 2020 02:54:15: 25000000 INFO @ Thu, 16 Apr 2020 02:54:20: 26000000 INFO @ Thu, 16 Apr 2020 02:54:21: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:54:25: 27000000 INFO @ Thu, 16 Apr 2020 02:54:29: 28000000 INFO @ Thu, 16 Apr 2020 02:54:31: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:54:31: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:54:31: #1 total tags in treatment: 28392351 INFO @ Thu, 16 Apr 2020 02:54:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:54:31: #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 02:54:32: #1 tags after filtering in treatment: 28392351 INFO @ Thu, 16 Apr 2020 02:54:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:54:32: #1 finished! INFO @ Thu, 16 Apr 2020 02:54:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:54:33: #2 number of paired peaks: 447 WARNING @ Thu, 16 Apr 2020 02:54:33: Fewer paired peaks (447) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 447 pairs to build model! INFO @ Thu, 16 Apr 2020 02:54:33: start model_add_line... INFO @ Thu, 16 Apr 2020 02:54:34: start X-correlation... INFO @ Thu, 16 Apr 2020 02:54:34: end of X-cor INFO @ Thu, 16 Apr 2020 02:54:34: #2 finished! INFO @ Thu, 16 Apr 2020 02:54:34: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:54:34: #2 alternative fragment length(s) may be 1,43,559,562 bps INFO @ Thu, 16 Apr 2020 02:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.20_model.r WARNING @ Thu, 16 Apr 2020 02:54:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:54:34: #2 You may need to consider one of the other alternative d(s): 1,43,559,562 WARNING @ Thu, 16 Apr 2020 02:54:34: #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 02:54:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.05_summits.bed INFO @ Thu, 16 Apr 2020 02:54:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:54:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.10_summits.bed INFO @ Thu, 16 Apr 2020 02:55:14: Done! INFO @ Thu, 16 Apr 2020 02:55:17: #3 Call peaks for each chromosome... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:55:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:55:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:55:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436050/SRX5436050.20_summits.bed INFO @ Thu, 16 Apr 2020 02:55:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。