Job ID = 12264754 SRX = SRX2969572 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30977986 spots for SRR5772135/SRR5772135.sra Written 30977986 spots for SRR5772135/SRR5772135.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265126 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:04 30977986 reads; of these: 30977986 (100.00%) were unpaired; of these: 1709850 (5.52%) aligned 0 times 25358146 (81.86%) aligned exactly 1 time 3909990 (12.62%) aligned >1 times 94.48% overall alignment rate Time searching: 00:09:05 Overall time: 00:09:05 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 12 files... [bam_rmdupse_core] 15320094 / 29268136 = 0.5234 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:10:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.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 @ Sat, 03 Apr 2021 06:10:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:10:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:10:41: 1000000 INFO @ Sat, 03 Apr 2021 06:10:51: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.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 @ Sat, 03 Apr 2021 06:11:00: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:00: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:01: 3000000 INFO @ Sat, 03 Apr 2021 06:11:11: 4000000 INFO @ Sat, 03 Apr 2021 06:11:11: 1000000 INFO @ Sat, 03 Apr 2021 06:11:20: 5000000 INFO @ Sat, 03 Apr 2021 06:11:21: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:11:30: 3000000 INFO @ Sat, 03 Apr 2021 06:11:30: 6000000 INFO @ Sat, 03 Apr 2021 06:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.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 @ Sat, 03 Apr 2021 06:11:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:39: 4000000 INFO @ Sat, 03 Apr 2021 06:11:39: 7000000 INFO @ Sat, 03 Apr 2021 06:11:39: 1000000 INFO @ Sat, 03 Apr 2021 06:11:47: 5000000 INFO @ Sat, 03 Apr 2021 06:11:49: 8000000 INFO @ Sat, 03 Apr 2021 06:11:49: 2000000 INFO @ Sat, 03 Apr 2021 06:11:56: 6000000 INFO @ Sat, 03 Apr 2021 06:11:58: 3000000 INFO @ Sat, 03 Apr 2021 06:11:58: 9000000 INFO @ Sat, 03 Apr 2021 06:12:05: 7000000 INFO @ Sat, 03 Apr 2021 06:12:06: 4000000 INFO @ Sat, 03 Apr 2021 06:12:07: 10000000 INFO @ Sat, 03 Apr 2021 06:12:13: 8000000 INFO @ Sat, 03 Apr 2021 06:12:15: 5000000 INFO @ Sat, 03 Apr 2021 06:12:16: 11000000 INFO @ Sat, 03 Apr 2021 06:12:22: 9000000 INFO @ Sat, 03 Apr 2021 06:12:24: 6000000 INFO @ Sat, 03 Apr 2021 06:12:25: 12000000 INFO @ Sat, 03 Apr 2021 06:12:31: 10000000 INFO @ Sat, 03 Apr 2021 06:12:32: 7000000 INFO @ Sat, 03 Apr 2021 06:12:34: 13000000 INFO @ Sat, 03 Apr 2021 06:12:39: 11000000 INFO @ Sat, 03 Apr 2021 06:12:41: 8000000 INFO @ Sat, 03 Apr 2021 06:12:43: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:12:43: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:12:43: #1 total tags in treatment: 13948042 INFO @ Sat, 03 Apr 2021 06:12:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:12:43: #1 tags after filtering in treatment: 13948042 INFO @ Sat, 03 Apr 2021 06:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:12:43: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:44: #2 number of paired peaks: 175 WARNING @ Sat, 03 Apr 2021 06:12:44: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 03 Apr 2021 06:12:44: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:44: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:44: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:44: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:44: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Apr 2021 06:12:44: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 03 Apr 2021 06:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.05_model.r WARNING @ Sat, 03 Apr 2021 06:12:44: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:44: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 03 Apr 2021 06:12:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:12:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:12:48: 12000000 INFO @ Sat, 03 Apr 2021 06:12:49: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:12:56: 13000000 INFO @ Sat, 03 Apr 2021 06:12:58: 10000000 INFO @ Sat, 03 Apr 2021 06:13:04: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:13:04: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:13:04: #1 total tags in treatment: 13948042 INFO @ Sat, 03 Apr 2021 06:13:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:13:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:13:05: #1 tags after filtering in treatment: 13948042 INFO @ Sat, 03 Apr 2021 06:13:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:13:05: #1 finished! INFO @ Sat, 03 Apr 2021 06:13:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:13:06: #2 number of paired peaks: 175 WARNING @ Sat, 03 Apr 2021 06:13:06: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 03 Apr 2021 06:13:06: start model_add_line... INFO @ Sat, 03 Apr 2021 06:13:06: start X-correlation... INFO @ Sat, 03 Apr 2021 06:13:06: end of X-cor INFO @ Sat, 03 Apr 2021 06:13:06: #2 finished! INFO @ Sat, 03 Apr 2021 06:13:06: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Apr 2021 06:13:06: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 03 Apr 2021 06:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.10_model.r WARNING @ Sat, 03 Apr 2021 06:13:06: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:13:06: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 03 Apr 2021 06:13:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:13:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:13:07: 11000000 INFO @ Sat, 03 Apr 2021 06:13:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:13:15: 12000000 INFO @ Sat, 03 Apr 2021 06:13:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:13:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:13:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.05_summits.bed INFO @ Sat, 03 Apr 2021 06:13:22: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4990 records, 4 fields): 94 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:13:24: 13000000 INFO @ Sat, 03 Apr 2021 06:13:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:13:32: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:13:32: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:13:32: #1 total tags in treatment: 13948042 INFO @ Sat, 03 Apr 2021 06:13:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:13:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:13:32: #1 tags after filtering in treatment: 13948042 INFO @ Sat, 03 Apr 2021 06:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:13:32: #1 finished! INFO @ Sat, 03 Apr 2021 06:13:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:13:33: #2 number of paired peaks: 175 WARNING @ Sat, 03 Apr 2021 06:13:33: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 03 Apr 2021 06:13:33: start model_add_line... INFO @ Sat, 03 Apr 2021 06:13:33: start X-correlation... INFO @ Sat, 03 Apr 2021 06:13:33: end of X-cor INFO @ Sat, 03 Apr 2021 06:13:33: #2 finished! INFO @ Sat, 03 Apr 2021 06:13:33: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Apr 2021 06:13:33: #2 alternative fragment length(s) may be 3,55 bps INFO @ Sat, 03 Apr 2021 06:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.20_model.r WARNING @ Sat, 03 Apr 2021 06:13:33: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:13:33: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Sat, 03 Apr 2021 06:13:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:13:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:13:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:13:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.10_summits.bed INFO @ Sat, 03 Apr 2021 06:13:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2392 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:13:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:14:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:14:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:14:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2969572/SRX2969572.20_summits.bed INFO @ Sat, 03 Apr 2021 06:14:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 2 millis CompletedMACS2peakCalling