Job ID = 12264791 SRX = SRX4082397 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14514202 spots for SRR7164229/SRR7164229.sra Written 14514202 spots for SRR7164229/SRR7164229.sra Read 21762988 spots for SRR7164230/SRR7164230.sra Written 21762988 spots for SRR7164230/SRR7164230.sra Read 2822618 spots for SRR7164231/SRR7164231.sra Written 2822618 spots for SRR7164231/SRR7164231.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265138 ("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: 00:08:01 39099808 reads; of these: 39099808 (100.00%) were unpaired; of these: 8825917 (22.57%) aligned 0 times 26714922 (68.32%) aligned exactly 1 time 3558969 (9.10%) aligned >1 times 77.43% overall alignment rate Time searching: 00:08:01 Overall time: 00:08:01 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] 16637849 / 30273891 = 0.5496 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 06:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.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 06:10:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:10:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:10:40: 1000000 INFO @ Sat, 03 Apr 2021 06:10:46: 2000000 INFO @ Sat, 03 Apr 2021 06:10:52: 3000000 INFO @ Sat, 03 Apr 2021 06:10:58: 4000000 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 06:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.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 06:11:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:04: 5000000 INFO @ Sat, 03 Apr 2021 06:11:10: 1000000 INFO @ Sat, 03 Apr 2021 06:11:10: 6000000 INFO @ Sat, 03 Apr 2021 06:11:16: 2000000 INFO @ Sat, 03 Apr 2021 06:11:17: 7000000 INFO @ Sat, 03 Apr 2021 06:11:22: 3000000 INFO @ Sat, 03 Apr 2021 06:11:23: 8000000 INFO @ Sat, 03 Apr 2021 06:11:28: 4000000 INFO @ Sat, 03 Apr 2021 06:11:29: 9000000 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 06:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.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 06:11:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:35: 5000000 INFO @ Sat, 03 Apr 2021 06:11:36: 10000000 INFO @ Sat, 03 Apr 2021 06:11:41: 1000000 INFO @ Sat, 03 Apr 2021 06:11:41: 6000000 INFO @ Sat, 03 Apr 2021 06:11:43: 11000000 INFO @ Sat, 03 Apr 2021 06:11:47: 2000000 INFO @ Sat, 03 Apr 2021 06:11:47: 7000000 INFO @ Sat, 03 Apr 2021 06:11:49: 12000000 INFO @ Sat, 03 Apr 2021 06:11:53: 3000000 INFO @ Sat, 03 Apr 2021 06:11:54: 8000000 INFO @ Sat, 03 Apr 2021 06:11:55: 13000000 INFO @ Sat, 03 Apr 2021 06:11:59: 4000000 INFO @ Sat, 03 Apr 2021 06:12:00: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:12:00: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:12:00: #1 total tags in treatment: 13636042 INFO @ Sat, 03 Apr 2021 06:12:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:00: #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 06:12:00: #1 tags after filtering in treatment: 13636042 INFO @ Sat, 03 Apr 2021 06:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:12:00: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:00: 9000000 INFO @ Sat, 03 Apr 2021 06:12:01: #2 number of paired peaks: 814 WARNING @ Sat, 03 Apr 2021 06:12:01: Fewer paired peaks (814) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 814 pairs to build model! INFO @ Sat, 03 Apr 2021 06:12:01: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:01: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:01: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:01: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:01: #2 predicted fragment length is 67 bps INFO @ Sat, 03 Apr 2021 06:12:01: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 03 Apr 2021 06:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.05_model.r WARNING @ Sat, 03 Apr 2021 06:12:01: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:01: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 03 Apr 2021 06:12:01: #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 06:12:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:12:05: 5000000 INFO @ Sat, 03 Apr 2021 06:12:06: 10000000 INFO @ Sat, 03 Apr 2021 06:12:11: 6000000 INFO @ Sat, 03 Apr 2021 06:12:12: 11000000 INFO @ Sat, 03 Apr 2021 06:12:18: 7000000 INFO @ Sat, 03 Apr 2021 06:12:19: 12000000 INFO @ Sat, 03 Apr 2021 06:12:24: 8000000 INFO @ Sat, 03 Apr 2021 06:12:25: 13000000 INFO @ Sat, 03 Apr 2021 06:12:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:12:29: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:12:29: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:12:29: #1 total tags in treatment: 13636042 INFO @ Sat, 03 Apr 2021 06:12:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:29: #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 06:12:29: #1 tags after filtering in treatment: 13636042 INFO @ Sat, 03 Apr 2021 06:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:12:29: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:30: #2 number of paired peaks: 814 WARNING @ Sat, 03 Apr 2021 06:12:30: Fewer paired peaks (814) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 814 pairs to build model! INFO @ Sat, 03 Apr 2021 06:12:30: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:30: 9000000 INFO @ Sat, 03 Apr 2021 06:12:30: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:30: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:30: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:30: #2 predicted fragment length is 67 bps INFO @ Sat, 03 Apr 2021 06:12:30: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 03 Apr 2021 06:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.10_model.r WARNING @ Sat, 03 Apr 2021 06:12:30: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:30: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 03 Apr 2021 06:12:30: #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 06:12:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:12:36: 10000000 INFO @ Sat, 03 Apr 2021 06:12:42: 11000000 INFO @ Sat, 03 Apr 2021 06:12:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:12:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.05_summits.bed INFO @ Sat, 03 Apr 2021 06:12:43: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (14917 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:12:47: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:12:52: 13000000 INFO @ Sat, 03 Apr 2021 06:12:56: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:12:56: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:12:56: #1 total tags in treatment: 13636042 INFO @ Sat, 03 Apr 2021 06:12:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:56: #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 06:12:56: #1 tags after filtering in treatment: 13636042 INFO @ Sat, 03 Apr 2021 06:12:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:12:56: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:12:57: #2 number of paired peaks: 814 WARNING @ Sat, 03 Apr 2021 06:12:57: Fewer paired peaks (814) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 814 pairs to build model! INFO @ Sat, 03 Apr 2021 06:12:57: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:57: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:57: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:57: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:57: #2 predicted fragment length is 67 bps INFO @ Sat, 03 Apr 2021 06:12:57: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 03 Apr 2021 06:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.20_model.r WARNING @ Sat, 03 Apr 2021 06:12:57: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:57: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 03 Apr 2021 06:12:57: #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 06:12:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:13:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:13:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:13:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.10_summits.bed INFO @ Sat, 03 Apr 2021 06:13:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9456 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:13:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082397/SRX4082397.20_summits.bed INFO @ Sat, 03 Apr 2021 06:13:35: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4155 records, 4 fields): 13 millis CompletedMACS2peakCalling