Job ID = 10165636 SRX = SRX6799193 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 37378121 spots for SRR10065400/SRR10065400.sra Written 37378121 spots for SRR10065400/SRR10065400.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165916 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:53 37378121 reads; of these: 37378121 (100.00%) were unpaired; of these: 1962851 (5.25%) aligned 0 times 25265945 (67.60%) aligned exactly 1 time 10149325 (27.15%) aligned >1 times 94.75% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 11215970 / 35415270 = 0.3167 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, 08 Oct 2020 19:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.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 @ Thu, 08 Oct 2020 19:48:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:44: 1000000 INFO @ Thu, 08 Oct 2020 19:48:49: 2000000 INFO @ Thu, 08 Oct 2020 19:48:54: 3000000 INFO @ Thu, 08 Oct 2020 19:48:58: 4000000 INFO @ Thu, 08 Oct 2020 19:49:03: 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, 08 Oct 2020 19:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.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 @ Thu, 08 Oct 2020 19:49:07: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:49:07: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:49:08: 6000000 INFO @ Thu, 08 Oct 2020 19:49:12: 1000000 INFO @ Thu, 08 Oct 2020 19:49:13: 7000000 INFO @ Thu, 08 Oct 2020 19:49:17: 2000000 INFO @ Thu, 08 Oct 2020 19:49:18: 8000000 INFO @ Thu, 08 Oct 2020 19:49:23: 3000000 INFO @ Thu, 08 Oct 2020 19:49:23: 9000000 INFO @ Thu, 08 Oct 2020 19:49:28: 4000000 INFO @ Thu, 08 Oct 2020 19:49:28: 10000000 INFO @ Thu, 08 Oct 2020 19:49:33: 5000000 INFO @ Thu, 08 Oct 2020 19:49:33: 11000000 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, 08 Oct 2020 19:49:38: 6000000 INFO @ Thu, 08 Oct 2020 19:49:38: 12000000 INFO @ Thu, 08 Oct 2020 19:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.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 @ Thu, 08 Oct 2020 19:49:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:49:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:49:43: 7000000 INFO @ Thu, 08 Oct 2020 19:49:43: 13000000 INFO @ Thu, 08 Oct 2020 19:49:44: 1000000 INFO @ Thu, 08 Oct 2020 19:49:48: 8000000 INFO @ Thu, 08 Oct 2020 19:49:48: 14000000 INFO @ Thu, 08 Oct 2020 19:49:49: 2000000 INFO @ Thu, 08 Oct 2020 19:49:53: 9000000 INFO @ Thu, 08 Oct 2020 19:49:54: 15000000 INFO @ Thu, 08 Oct 2020 19:49:55: 3000000 INFO @ Thu, 08 Oct 2020 19:49:58: 10000000 INFO @ Thu, 08 Oct 2020 19:49:59: 16000000 INFO @ Thu, 08 Oct 2020 19:50:00: 4000000 INFO @ Thu, 08 Oct 2020 19:50:03: 11000000 INFO @ Thu, 08 Oct 2020 19:50:04: 17000000 INFO @ Thu, 08 Oct 2020 19:50:05: 5000000 INFO @ Thu, 08 Oct 2020 19:50:08: 12000000 INFO @ Thu, 08 Oct 2020 19:50:09: 18000000 INFO @ Thu, 08 Oct 2020 19:50:10: 6000000 INFO @ Thu, 08 Oct 2020 19:50:13: 13000000 INFO @ Thu, 08 Oct 2020 19:50:14: 19000000 INFO @ Thu, 08 Oct 2020 19:50:15: 7000000 INFO @ Thu, 08 Oct 2020 19:50:19: 14000000 INFO @ Thu, 08 Oct 2020 19:50:20: 20000000 INFO @ Thu, 08 Oct 2020 19:50:20: 8000000 INFO @ Thu, 08 Oct 2020 19:50:24: 15000000 INFO @ Thu, 08 Oct 2020 19:50:25: 21000000 INFO @ Thu, 08 Oct 2020 19:50:25: 9000000 INFO @ Thu, 08 Oct 2020 19:50:30: 16000000 INFO @ Thu, 08 Oct 2020 19:50:30: 22000000 INFO @ Thu, 08 Oct 2020 19:50:30: 10000000 INFO @ Thu, 08 Oct 2020 19:50:35: 17000000 INFO @ Thu, 08 Oct 2020 19:50:35: 23000000 INFO @ Thu, 08 Oct 2020 19:50:35: 11000000 INFO @ Thu, 08 Oct 2020 19:50:40: 18000000 INFO @ Thu, 08 Oct 2020 19:50:40: 24000000 INFO @ Thu, 08 Oct 2020 19:50:40: 12000000 INFO @ Thu, 08 Oct 2020 19:50:41: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:41: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:41: #1 total tags in treatment: 24199300 INFO @ Thu, 08 Oct 2020 19:50:41: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:42: #1 tags after filtering in treatment: 24199300 INFO @ Thu, 08 Oct 2020 19:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:42: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:42: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:43: #2 number of paired peaks: 318 WARNING @ Thu, 08 Oct 2020 19:50:43: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:43: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:44: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:44: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:44: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:44: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:50:44: #2 alternative fragment length(s) may be 1,11 bps INFO @ Thu, 08 Oct 2020 19:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05_model.r WARNING @ Thu, 08 Oct 2020 19:50:44: #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, 08 Oct 2020 19:50:44: #2 You may need to consider one of the other alternative d(s): 1,11 WARNING @ Thu, 08 Oct 2020 19:50:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:50:44: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:45: 19000000 INFO @ Thu, 08 Oct 2020 19:50:46: 13000000 INFO @ Thu, 08 Oct 2020 19:50:50: 20000000 INFO @ Thu, 08 Oct 2020 19:50:51: 14000000 INFO @ Thu, 08 Oct 2020 19:50:55: 21000000 INFO @ Thu, 08 Oct 2020 19:50:56: 15000000 INFO @ Thu, 08 Oct 2020 19:51:01: 22000000 INFO @ Thu, 08 Oct 2020 19:51:01: 16000000 INFO @ Thu, 08 Oct 2020 19:51:06: 23000000 INFO @ Thu, 08 Oct 2020 19:51:06: 17000000 INFO @ Thu, 08 Oct 2020 19:51:11: 24000000 INFO @ Thu, 08 Oct 2020 19:51:11: 18000000 INFO @ Thu, 08 Oct 2020 19:51:12: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:51:12: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:51:12: #1 total tags in treatment: 24199300 INFO @ Thu, 08 Oct 2020 19:51:12: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:51:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:51:12: #1 tags after filtering in treatment: 24199300 INFO @ Thu, 08 Oct 2020 19:51:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:51:12: #1 finished! INFO @ Thu, 08 Oct 2020 19:51:12: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:51:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:51:14: #2 number of paired peaks: 318 WARNING @ Thu, 08 Oct 2020 19:51:14: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Thu, 08 Oct 2020 19:51:14: start model_add_line... INFO @ Thu, 08 Oct 2020 19:51:14: start X-correlation... INFO @ Thu, 08 Oct 2020 19:51:14: end of X-cor INFO @ Thu, 08 Oct 2020 19:51:14: #2 finished! INFO @ Thu, 08 Oct 2020 19:51:14: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:51:14: #2 alternative fragment length(s) may be 1,11 bps INFO @ Thu, 08 Oct 2020 19:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10_model.r WARNING @ Thu, 08 Oct 2020 19:51:14: #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, 08 Oct 2020 19:51:14: #2 You may need to consider one of the other alternative d(s): 1,11 WARNING @ Thu, 08 Oct 2020 19:51:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:51:14: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:51:16: 19000000 INFO @ Thu, 08 Oct 2020 19:51:19: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:21: 20000000 INFO @ Thu, 08 Oct 2020 19:51:26: 21000000 INFO @ Thu, 08 Oct 2020 19:51:31: 22000000 INFO @ Thu, 08 Oct 2020 19:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.05_summits.bed INFO @ Thu, 08 Oct 2020 19:51:35: Done! INFO @ Thu, 08 Oct 2020 19:51:36: 23000000 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... INFO @ Thu, 08 Oct 2020 19:51:41: 24000000 INFO @ Thu, 08 Oct 2020 19:51:42: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:51:42: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:51:42: #1 total tags in treatment: 24199300 INFO @ Thu, 08 Oct 2020 19:51:42: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:51:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:51:43: #1 tags after filtering in treatment: 24199300 INFO @ Thu, 08 Oct 2020 19:51:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:51:43: #1 finished! INFO @ Thu, 08 Oct 2020 19:51:43: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:51:44: #2 number of paired peaks: 318 WARNING @ Thu, 08 Oct 2020 19:51:44: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Thu, 08 Oct 2020 19:51:44: start model_add_line... INFO @ Thu, 08 Oct 2020 19:51:45: start X-correlation... INFO @ Thu, 08 Oct 2020 19:51:45: end of X-cor INFO @ Thu, 08 Oct 2020 19:51:45: #2 finished! INFO @ Thu, 08 Oct 2020 19:51:45: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:51:45: #2 alternative fragment length(s) may be 1,11 bps INFO @ Thu, 08 Oct 2020 19:51:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20_model.r WARNING @ Thu, 08 Oct 2020 19:51:45: #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, 08 Oct 2020 19:51:45: #2 You may need to consider one of the other alternative d(s): 1,11 WARNING @ Thu, 08 Oct 2020 19:51:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:51:45: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:51:49: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.10_summits.bed INFO @ Thu, 08 Oct 2020 19:52:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:52:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799193/SRX6799193.20_summits.bed INFO @ Thu, 08 Oct 2020 19:52:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling