Job ID = 12264793 SRX = SRX4082399 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 85494043 spots for SRR7164234/SRR7164234.sra Written 85494043 spots for SRR7164234/SRR7164234.sra Read 70451403 spots for SRR7164235/SRR7164235.sra Written 70451403 spots for SRR7164235/SRR7164235.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265380 ("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: 00:18:36 155945446 reads; of these: 155945446 (100.00%) were unpaired; of these: 102459080 (65.70%) aligned 0 times 47193153 (30.26%) aligned exactly 1 time 6293213 (4.04%) aligned >1 times 34.30% overall alignment rate Time searching: 00:18:36 Overall time: 00:18:36 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 24 files... [bam_rmdupse_core] 35448257 / 53486366 = 0.6628 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 06:35:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.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 06:35:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:35:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:35:15: 1000000 INFO @ Sat, 03 Apr 2021 06:35:21: 2000000 INFO @ Sat, 03 Apr 2021 06:35:27: 3000000 INFO @ Sat, 03 Apr 2021 06:35:34: 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 06:35:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.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 06:35:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:35:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:35:40: 5000000 INFO @ Sat, 03 Apr 2021 06:35:44: 1000000 INFO @ Sat, 03 Apr 2021 06:35:47: 6000000 INFO @ Sat, 03 Apr 2021 06:35:51: 2000000 INFO @ Sat, 03 Apr 2021 06:35:53: 7000000 INFO @ Sat, 03 Apr 2021 06:35:58: 3000000 INFO @ Sat, 03 Apr 2021 06:36:00: 8000000 INFO @ Sat, 03 Apr 2021 06:36:04: 4000000 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 06:36:07: 9000000 INFO @ Sat, 03 Apr 2021 06:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.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 06:36:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:36:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:36:12: 5000000 INFO @ Sat, 03 Apr 2021 06:36:14: 10000000 INFO @ Sat, 03 Apr 2021 06:36:15: 1000000 INFO @ Sat, 03 Apr 2021 06:36:19: 6000000 INFO @ Sat, 03 Apr 2021 06:36:20: 11000000 INFO @ Sat, 03 Apr 2021 06:36:22: 2000000 INFO @ Sat, 03 Apr 2021 06:36:25: 7000000 INFO @ Sat, 03 Apr 2021 06:36:27: 12000000 INFO @ Sat, 03 Apr 2021 06:36:29: 3000000 INFO @ Sat, 03 Apr 2021 06:36:33: 8000000 INFO @ Sat, 03 Apr 2021 06:36:34: 13000000 INFO @ Sat, 03 Apr 2021 06:36:36: 4000000 INFO @ Sat, 03 Apr 2021 06:36:40: 9000000 INFO @ Sat, 03 Apr 2021 06:36:40: 14000000 INFO @ Sat, 03 Apr 2021 06:36:44: 5000000 INFO @ Sat, 03 Apr 2021 06:36:46: 10000000 INFO @ Sat, 03 Apr 2021 06:36:47: 15000000 INFO @ Sat, 03 Apr 2021 06:36:51: 6000000 INFO @ Sat, 03 Apr 2021 06:36:53: 11000000 INFO @ Sat, 03 Apr 2021 06:36:54: 16000000 INFO @ Sat, 03 Apr 2021 06:36:57: 7000000 INFO @ Sat, 03 Apr 2021 06:36:59: 12000000 INFO @ Sat, 03 Apr 2021 06:37:00: 17000000 INFO @ Sat, 03 Apr 2021 06:37:04: 8000000 INFO @ Sat, 03 Apr 2021 06:37:06: 13000000 INFO @ Sat, 03 Apr 2021 06:37:07: 18000000 INFO @ Sat, 03 Apr 2021 06:37:07: #1 tag size is determined as 48 bps INFO @ Sat, 03 Apr 2021 06:37:07: #1 tag size = 48 INFO @ Sat, 03 Apr 2021 06:37:07: #1 total tags in treatment: 18038109 INFO @ Sat, 03 Apr 2021 06:37:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:37:07: #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 06:37:08: #1 tags after filtering in treatment: 18038109 INFO @ Sat, 03 Apr 2021 06:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:37:08: #1 finished! INFO @ Sat, 03 Apr 2021 06:37:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:37:09: #2 number of paired peaks: 499 WARNING @ Sat, 03 Apr 2021 06:37:09: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Sat, 03 Apr 2021 06:37:09: start model_add_line... INFO @ Sat, 03 Apr 2021 06:37:09: start X-correlation... INFO @ Sat, 03 Apr 2021 06:37:09: end of X-cor INFO @ Sat, 03 Apr 2021 06:37:09: #2 finished! INFO @ Sat, 03 Apr 2021 06:37:09: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 06:37:09: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 06:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.05_model.r WARNING @ Sat, 03 Apr 2021 06:37:09: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:37:09: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 06:37:09: #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 06:37:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:37:11: 9000000 INFO @ Sat, 03 Apr 2021 06:37:12: 14000000 INFO @ Sat, 03 Apr 2021 06:37:17: 10000000 INFO @ Sat, 03 Apr 2021 06:37:18: 15000000 INFO @ Sat, 03 Apr 2021 06:37:23: 11000000 INFO @ Sat, 03 Apr 2021 06:37:25: 16000000 INFO @ Sat, 03 Apr 2021 06:37:30: 12000000 INFO @ Sat, 03 Apr 2021 06:37:32: 17000000 INFO @ Sat, 03 Apr 2021 06:37:37: 13000000 INFO @ Sat, 03 Apr 2021 06:37:38: 18000000 INFO @ Sat, 03 Apr 2021 06:37:38: #1 tag size is determined as 48 bps INFO @ Sat, 03 Apr 2021 06:37:38: #1 tag size = 48 INFO @ Sat, 03 Apr 2021 06:37:38: #1 total tags in treatment: 18038109 INFO @ Sat, 03 Apr 2021 06:37:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:37:38: #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 06:37:39: #1 tags after filtering in treatment: 18038109 INFO @ Sat, 03 Apr 2021 06:37:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:37:39: #1 finished! INFO @ Sat, 03 Apr 2021 06:37:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:37:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:37:40: #2 number of paired peaks: 499 WARNING @ Sat, 03 Apr 2021 06:37:40: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Sat, 03 Apr 2021 06:37:40: start model_add_line... INFO @ Sat, 03 Apr 2021 06:37:40: start X-correlation... INFO @ Sat, 03 Apr 2021 06:37:40: end of X-cor INFO @ Sat, 03 Apr 2021 06:37:40: #2 finished! INFO @ Sat, 03 Apr 2021 06:37:40: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 06:37:40: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 06:37:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.10_model.r WARNING @ Sat, 03 Apr 2021 06:37:40: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:37:40: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 06:37:40: #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 06:37:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:37:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:37:43: 14000000 INFO @ Sat, 03 Apr 2021 06:37:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:37:48: 15000000 INFO @ Sat, 03 Apr 2021 06:37:55: 16000000 INFO @ Sat, 03 Apr 2021 06:38:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:38:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:38:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.05_summits.bed INFO @ Sat, 03 Apr 2021 06:38:01: Done! INFO @ Sat, 03 Apr 2021 06:38:01: 17000000 pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (17850 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:38:07: 18000000 INFO @ Sat, 03 Apr 2021 06:38:07: #1 tag size is determined as 48 bps INFO @ Sat, 03 Apr 2021 06:38:07: #1 tag size = 48 INFO @ Sat, 03 Apr 2021 06:38:07: #1 total tags in treatment: 18038109 INFO @ Sat, 03 Apr 2021 06:38:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:38:07: #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 06:38:08: #1 tags after filtering in treatment: 18038109 INFO @ Sat, 03 Apr 2021 06:38:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:38:08: #1 finished! INFO @ Sat, 03 Apr 2021 06:38:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:38:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:38:09: #2 number of paired peaks: 499 WARNING @ Sat, 03 Apr 2021 06:38:09: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Sat, 03 Apr 2021 06:38:09: start model_add_line... INFO @ Sat, 03 Apr 2021 06:38:09: start X-correlation... INFO @ Sat, 03 Apr 2021 06:38:09: end of X-cor INFO @ Sat, 03 Apr 2021 06:38:09: #2 finished! INFO @ Sat, 03 Apr 2021 06:38:09: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 06:38:09: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 06:38:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.20_model.r WARNING @ Sat, 03 Apr 2021 06:38:09: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:38:09: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 06:38:09: #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 06:38:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:38:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:38:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:38:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:38:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.10_summits.bed INFO @ Sat, 03 Apr 2021 06:38:31: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (11668 records, 4 fields): 16 millis BigWig に変換しました。 CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:38:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:39:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:39:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:39:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082399/SRX4082399.20_summits.bed INFO @ Sat, 03 Apr 2021 06:39:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5163 records, 4 fields): 13 millis CompletedMACS2peakCalling