Job ID = 6367015 SRX = SRX2582954 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:13:46 prefetch.2.10.7: 1) Downloading 'SRR5279131'... 2020-06-15T23:13:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:14:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:14:38 prefetch.2.10.7: 'SRR5279131' is valid 2020-06-15T23:14:38 prefetch.2.10.7: 1) 'SRR5279131' was downloaded successfully 2020-06-15T23:14:38 prefetch.2.10.7: 'SRR5279131' has 0 unresolved dependencies Read 16504724 spots for SRR5279131/SRR5279131.sra Written 16504724 spots for SRR5279131/SRR5279131.sra 2020-06-15T23:15:49 prefetch.2.10.7: 1) Downloading 'SRR5279132'... 2020-06-15T23:15:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:16:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:16:51 prefetch.2.10.7: 'SRR5279132' is valid 2020-06-15T23:16:51 prefetch.2.10.7: 1) 'SRR5279132' was downloaded successfully 2020-06-15T23:16:51 prefetch.2.10.7: 'SRR5279132' has 0 unresolved dependencies Read 16253253 spots for SRR5279132/SRR5279132.sra Written 16253253 spots for SRR5279132/SRR5279132.sra 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: 00:07:27 32757977 reads; of these: 32757977 (100.00%) were unpaired; of these: 343295 (1.05%) aligned 0 times 27272191 (83.25%) aligned exactly 1 time 5142491 (15.70%) aligned >1 times 98.95% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 7147014 / 32414682 = 0.2205 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 @ Tue, 16 Jun 2020 08:32:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:32:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:32:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:03: 1000000 INFO @ Tue, 16 Jun 2020 08:33:08: 2000000 INFO @ Tue, 16 Jun 2020 08:33:13: 3000000 INFO @ Tue, 16 Jun 2020 08:33:19: 4000000 INFO @ Tue, 16 Jun 2020 08:33:24: 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 @ Tue, 16 Jun 2020 08:33:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:33:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:30: 6000000 INFO @ Tue, 16 Jun 2020 08:33:34: 1000000 INFO @ Tue, 16 Jun 2020 08:33:36: 7000000 INFO @ Tue, 16 Jun 2020 08:33:40: 2000000 INFO @ Tue, 16 Jun 2020 08:33:42: 8000000 INFO @ Tue, 16 Jun 2020 08:33:47: 3000000 INFO @ Tue, 16 Jun 2020 08:33:49: 9000000 INFO @ Tue, 16 Jun 2020 08:33:53: 4000000 INFO @ Tue, 16 Jun 2020 08:33:55: 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 @ Tue, 16 Jun 2020 08:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:33:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:00: 5000000 INFO @ Tue, 16 Jun 2020 08:34:01: 11000000 INFO @ Tue, 16 Jun 2020 08:34:04: 1000000 INFO @ Tue, 16 Jun 2020 08:34:06: 6000000 INFO @ Tue, 16 Jun 2020 08:34:08: 12000000 INFO @ Tue, 16 Jun 2020 08:34:10: 2000000 INFO @ Tue, 16 Jun 2020 08:34:13: 7000000 INFO @ Tue, 16 Jun 2020 08:34:14: 13000000 INFO @ Tue, 16 Jun 2020 08:34:17: 3000000 INFO @ Tue, 16 Jun 2020 08:34:19: 8000000 INFO @ Tue, 16 Jun 2020 08:34:20: 14000000 INFO @ Tue, 16 Jun 2020 08:34:23: 4000000 INFO @ Tue, 16 Jun 2020 08:34:25: 9000000 INFO @ Tue, 16 Jun 2020 08:34:27: 15000000 INFO @ Tue, 16 Jun 2020 08:34:29: 5000000 INFO @ Tue, 16 Jun 2020 08:34:31: 10000000 INFO @ Tue, 16 Jun 2020 08:34:33: 16000000 INFO @ Tue, 16 Jun 2020 08:34:35: 6000000 INFO @ Tue, 16 Jun 2020 08:34:38: 11000000 INFO @ Tue, 16 Jun 2020 08:34:39: 17000000 INFO @ Tue, 16 Jun 2020 08:34:41: 7000000 INFO @ Tue, 16 Jun 2020 08:34:45: 12000000 INFO @ Tue, 16 Jun 2020 08:34:46: 18000000 INFO @ Tue, 16 Jun 2020 08:34:47: 8000000 INFO @ Tue, 16 Jun 2020 08:34:51: 13000000 INFO @ Tue, 16 Jun 2020 08:34:52: 19000000 INFO @ Tue, 16 Jun 2020 08:34:53: 9000000 INFO @ Tue, 16 Jun 2020 08:34:57: 14000000 INFO @ Tue, 16 Jun 2020 08:34:58: 20000000 INFO @ Tue, 16 Jun 2020 08:35:00: 10000000 INFO @ Tue, 16 Jun 2020 08:35:03: 15000000 INFO @ Tue, 16 Jun 2020 08:35:04: 21000000 INFO @ Tue, 16 Jun 2020 08:35:06: 11000000 INFO @ Tue, 16 Jun 2020 08:35:10: 16000000 INFO @ Tue, 16 Jun 2020 08:35:11: 22000000 INFO @ Tue, 16 Jun 2020 08:35:12: 12000000 INFO @ Tue, 16 Jun 2020 08:35:16: 17000000 INFO @ Tue, 16 Jun 2020 08:35:17: 23000000 INFO @ Tue, 16 Jun 2020 08:35:18: 13000000 INFO @ Tue, 16 Jun 2020 08:35:22: 18000000 INFO @ Tue, 16 Jun 2020 08:35:24: 24000000 INFO @ Tue, 16 Jun 2020 08:35:24: 14000000 INFO @ Tue, 16 Jun 2020 08:35:28: 19000000 INFO @ Tue, 16 Jun 2020 08:35:30: 25000000 INFO @ Tue, 16 Jun 2020 08:35:30: 15000000 INFO @ Tue, 16 Jun 2020 08:35:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:35:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:35:32: #1 total tags in treatment: 25267668 INFO @ Tue, 16 Jun 2020 08:35:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:35:32: #1 tags after filtering in treatment: 25267668 INFO @ Tue, 16 Jun 2020 08:35:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:34: #2 number of paired peaks: 123 WARNING @ Tue, 16 Jun 2020 08:35:34: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:34: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:35:34: #2 alternative fragment length(s) may be 1,33,46,125,522,548,580 bps INFO @ Tue, 16 Jun 2020 08:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.05_model.r WARNING @ Tue, 16 Jun 2020 08:35:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:35:34: #2 You may need to consider one of the other alternative d(s): 1,33,46,125,522,548,580 WARNING @ Tue, 16 Jun 2020 08:35:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:35:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:35:34: 20000000 INFO @ Tue, 16 Jun 2020 08:35:36: 16000000 INFO @ Tue, 16 Jun 2020 08:35:40: 21000000 INFO @ Tue, 16 Jun 2020 08:35:42: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:35:46: 22000000 INFO @ Tue, 16 Jun 2020 08:35:48: 18000000 INFO @ Tue, 16 Jun 2020 08:35:52: 23000000 INFO @ Tue, 16 Jun 2020 08:35:54: 19000000 INFO @ Tue, 16 Jun 2020 08:35:59: 24000000 INFO @ Tue, 16 Jun 2020 08:36:00: 20000000 INFO @ Tue, 16 Jun 2020 08:36:05: 25000000 INFO @ Tue, 16 Jun 2020 08:36:06: 21000000 INFO @ Tue, 16 Jun 2020 08:36:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:36:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:36:07: #1 total tags in treatment: 25267668 INFO @ Tue, 16 Jun 2020 08:36:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:36:07: #1 tags after filtering in treatment: 25267668 INFO @ Tue, 16 Jun 2020 08:36:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:08: #2 number of paired peaks: 123 WARNING @ Tue, 16 Jun 2020 08:36:08: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:09: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:36:09: #2 alternative fragment length(s) may be 1,33,46,125,522,548,580 bps INFO @ Tue, 16 Jun 2020 08:36:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.10_model.r WARNING @ Tue, 16 Jun 2020 08:36:09: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:09: #2 You may need to consider one of the other alternative d(s): 1,33,46,125,522,548,580 WARNING @ Tue, 16 Jun 2020 08:36:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:36:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:12: 22000000 INFO @ Tue, 16 Jun 2020 08:36:18: 23000000 INFO @ Tue, 16 Jun 2020 08:36:23: 24000000 INFO @ Tue, 16 Jun 2020 08:36:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:29: 25000000 INFO @ Tue, 16 Jun 2020 08:36:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:36:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:36:31: #1 total tags in treatment: 25267668 INFO @ Tue, 16 Jun 2020 08:36:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:36:31: #1 tags after filtering in treatment: 25267668 INFO @ Tue, 16 Jun 2020 08:36:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:33: #2 number of paired peaks: 123 WARNING @ Tue, 16 Jun 2020 08:36:33: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:33: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:36:33: #2 alternative fragment length(s) may be 1,33,46,125,522,548,580 bps INFO @ Tue, 16 Jun 2020 08:36:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.20_model.r WARNING @ Tue, 16 Jun 2020 08:36:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:33: #2 You may need to consider one of the other alternative d(s): 1,33,46,125,522,548,580 WARNING @ Tue, 16 Jun 2020 08:36:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:36:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:36:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2582954/SRX2582954.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:27: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling