Job ID = 14160423 SRX = SRX8151892 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13926243 spots for SRR11584270/SRR11584270.sra Written 13926243 spots for SRR11584270/SRR11584270.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160559 ("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: 00:03:32 13926243 reads; of these: 13926243 (100.00%) were unpaired; of these: 872886 (6.27%) aligned 0 times 10890919 (78.20%) aligned exactly 1 time 2162438 (15.53%) aligned >1 times 93.73% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 929604 / 13053357 = 0.0712 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:30:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.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, 09 Dec 2021 02:30:49: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:30:49: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:30:57: 1000000 INFO @ Thu, 09 Dec 2021 02:31:05: 2000000 INFO @ Thu, 09 Dec 2021 02:31:13: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:31:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.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, 09 Dec 2021 02:31:19: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:31:19: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:31:20: 4000000 INFO @ Thu, 09 Dec 2021 02:31:26: 1000000 INFO @ Thu, 09 Dec 2021 02:31:27: 5000000 INFO @ Thu, 09 Dec 2021 02:31:34: 2000000 INFO @ Thu, 09 Dec 2021 02:31:35: 6000000 INFO @ Thu, 09 Dec 2021 02:31:41: 3000000 INFO @ Thu, 09 Dec 2021 02:31:42: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:31:48: 4000000 INFO @ Thu, 09 Dec 2021 02:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.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, 09 Dec 2021 02:31:48: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:31:48: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:31:50: 8000000 INFO @ Thu, 09 Dec 2021 02:31:55: 1000000 INFO @ Thu, 09 Dec 2021 02:31:56: 5000000 INFO @ Thu, 09 Dec 2021 02:31:57: 9000000 INFO @ Thu, 09 Dec 2021 02:32:03: 2000000 INFO @ Thu, 09 Dec 2021 02:32:03: 6000000 INFO @ Thu, 09 Dec 2021 02:32:05: 10000000 INFO @ Thu, 09 Dec 2021 02:32:10: 3000000 INFO @ Thu, 09 Dec 2021 02:32:11: 7000000 INFO @ Thu, 09 Dec 2021 02:32:13: 11000000 INFO @ Thu, 09 Dec 2021 02:32:18: 4000000 INFO @ Thu, 09 Dec 2021 02:32:18: 8000000 INFO @ Thu, 09 Dec 2021 02:32:20: 12000000 INFO @ Thu, 09 Dec 2021 02:32:21: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:32:21: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:32:21: #1 total tags in treatment: 12123753 INFO @ Thu, 09 Dec 2021 02:32:21: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:32:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:32:21: #1 tags after filtering in treatment: 12123753 INFO @ Thu, 09 Dec 2021 02:32:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:32:21: #1 finished! INFO @ Thu, 09 Dec 2021 02:32:21: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:32:22: #2 number of paired peaks: 285 WARNING @ Thu, 09 Dec 2021 02:32:22: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 09 Dec 2021 02:32:22: start model_add_line... INFO @ Thu, 09 Dec 2021 02:32:22: start X-correlation... INFO @ Thu, 09 Dec 2021 02:32:23: end of X-cor INFO @ Thu, 09 Dec 2021 02:32:23: #2 finished! INFO @ Thu, 09 Dec 2021 02:32:23: #2 predicted fragment length is 43 bps INFO @ Thu, 09 Dec 2021 02:32:23: #2 alternative fragment length(s) may be 2,43,549,566 bps INFO @ Thu, 09 Dec 2021 02:32:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.05_model.r WARNING @ Thu, 09 Dec 2021 02:32:23: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:32:23: #2 You may need to consider one of the other alternative d(s): 2,43,549,566 WARNING @ Thu, 09 Dec 2021 02:32:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:32:23: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:32:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:32:25: 5000000 INFO @ Thu, 09 Dec 2021 02:32:25: 9000000 INFO @ Thu, 09 Dec 2021 02:32:31: 6000000 INFO @ Thu, 09 Dec 2021 02:32:32: 10000000 INFO @ Thu, 09 Dec 2021 02:32:38: 7000000 INFO @ Thu, 09 Dec 2021 02:32:39: 11000000 INFO @ Thu, 09 Dec 2021 02:32:44: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:32:46: 8000000 INFO @ Thu, 09 Dec 2021 02:32:46: 12000000 INFO @ Thu, 09 Dec 2021 02:32:47: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:32:47: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:32:47: #1 total tags in treatment: 12123753 INFO @ Thu, 09 Dec 2021 02:32:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:32:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:32:47: #1 tags after filtering in treatment: 12123753 INFO @ Thu, 09 Dec 2021 02:32:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:32:47: #1 finished! INFO @ Thu, 09 Dec 2021 02:32:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:32:48: #2 number of paired peaks: 285 WARNING @ Thu, 09 Dec 2021 02:32:48: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 09 Dec 2021 02:32:48: start model_add_line... INFO @ Thu, 09 Dec 2021 02:32:48: start X-correlation... INFO @ Thu, 09 Dec 2021 02:32:48: end of X-cor INFO @ Thu, 09 Dec 2021 02:32:48: #2 finished! INFO @ Thu, 09 Dec 2021 02:32:48: #2 predicted fragment length is 43 bps INFO @ Thu, 09 Dec 2021 02:32:48: #2 alternative fragment length(s) may be 2,43,549,566 bps INFO @ Thu, 09 Dec 2021 02:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.10_model.r WARNING @ Thu, 09 Dec 2021 02:32:48: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:32:48: #2 You may need to consider one of the other alternative d(s): 2,43,549,566 WARNING @ Thu, 09 Dec 2021 02:32:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:32:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:32:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:32:53: 9000000 INFO @ Thu, 09 Dec 2021 02:32:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:32:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:32:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.05_summits.bed INFO @ Thu, 09 Dec 2021 02:32:56: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (645 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:32:59: 10000000 INFO @ Thu, 09 Dec 2021 02:33:06: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:33:10: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:33:13: 12000000 INFO @ Thu, 09 Dec 2021 02:33:14: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 02:33:14: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 02:33:14: #1 total tags in treatment: 12123753 INFO @ Thu, 09 Dec 2021 02:33:14: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:33:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:33:14: #1 tags after filtering in treatment: 12123753 INFO @ Thu, 09 Dec 2021 02:33:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:33:14: #1 finished! INFO @ Thu, 09 Dec 2021 02:33:14: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:33:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:33:15: #2 number of paired peaks: 285 WARNING @ Thu, 09 Dec 2021 02:33:15: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 09 Dec 2021 02:33:15: start model_add_line... INFO @ Thu, 09 Dec 2021 02:33:15: start X-correlation... INFO @ Thu, 09 Dec 2021 02:33:16: end of X-cor INFO @ Thu, 09 Dec 2021 02:33:16: #2 finished! INFO @ Thu, 09 Dec 2021 02:33:16: #2 predicted fragment length is 43 bps INFO @ Thu, 09 Dec 2021 02:33:16: #2 alternative fragment length(s) may be 2,43,549,566 bps INFO @ Thu, 09 Dec 2021 02:33:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.20_model.r WARNING @ Thu, 09 Dec 2021 02:33:16: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:33:16: #2 You may need to consider one of the other alternative d(s): 2,43,549,566 WARNING @ Thu, 09 Dec 2021 02:33:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:33:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:33:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:33:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:33:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:33:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.10_summits.bed INFO @ Thu, 09 Dec 2021 02:33:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:33:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:33:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:33:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:33:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8151892/SRX8151892.20_summits.bed INFO @ Thu, 09 Dec 2021 02:33:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 2 millis CompletedMACS2peakCalling