Job ID = 12264789 SRX = SRX4082395 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12821981 spots for SRR7164224/SRR7164224.sra Written 12821981 spots for SRR7164224/SRR7164224.sra Read 42822528 spots for SRR7164225/SRR7164225.sra Written 42822528 spots for SRR7164225/SRR7164225.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265204 ("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: 00:11:40 55644509 reads; of these: 55644509 (100.00%) were unpaired; of these: 8374604 (15.05%) aligned 0 times 40663963 (73.08%) aligned exactly 1 time 6605942 (11.87%) aligned >1 times 84.95% overall alignment rate Time searching: 00:11:40 Overall time: 00:11:40 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 20 files... [bam_rmdupse_core] 33005952 / 47269905 = 0.6982 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 06:17:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.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 06:17:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:17:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:17:38: 1000000 INFO @ Sat, 03 Apr 2021 06:17:44: 2000000 INFO @ Sat, 03 Apr 2021 06:17:50: 3000000 INFO @ Sat, 03 Apr 2021 06:17:56: 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 06:18:01: 5000000 INFO @ Sat, 03 Apr 2021 06:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.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 06:18:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:18:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:18:08: 6000000 INFO @ Sat, 03 Apr 2021 06:18:08: 1000000 INFO @ Sat, 03 Apr 2021 06:18:14: 7000000 INFO @ Sat, 03 Apr 2021 06:18:15: 2000000 INFO @ Sat, 03 Apr 2021 06:18:21: 8000000 INFO @ Sat, 03 Apr 2021 06:18:21: 3000000 INFO @ Sat, 03 Apr 2021 06:18:28: 9000000 INFO @ Sat, 03 Apr 2021 06:18:28: 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 06:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.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 06:18:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:18:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:18:34: 10000000 INFO @ Sat, 03 Apr 2021 06:18:35: 5000000 INFO @ Sat, 03 Apr 2021 06:18:39: 1000000 INFO @ Sat, 03 Apr 2021 06:18:41: 11000000 INFO @ Sat, 03 Apr 2021 06:18:41: 6000000 INFO @ Sat, 03 Apr 2021 06:18:46: 2000000 INFO @ Sat, 03 Apr 2021 06:18:49: 12000000 INFO @ Sat, 03 Apr 2021 06:18:49: 7000000 INFO @ Sat, 03 Apr 2021 06:18:54: 3000000 INFO @ Sat, 03 Apr 2021 06:18:56: 13000000 INFO @ Sat, 03 Apr 2021 06:18:56: 8000000 INFO @ Sat, 03 Apr 2021 06:19:01: 4000000 INFO @ Sat, 03 Apr 2021 06:19:03: 14000000 INFO @ Sat, 03 Apr 2021 06:19:03: 9000000 INFO @ Sat, 03 Apr 2021 06:19:05: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 06:19:05: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 06:19:05: #1 total tags in treatment: 14263953 INFO @ Sat, 03 Apr 2021 06:19:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:05: #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 06:19:05: #1 tags after filtering in treatment: 14263953 INFO @ Sat, 03 Apr 2021 06:19:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:19:05: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:19:06: #2 number of paired peaks: 1279 INFO @ Sat, 03 Apr 2021 06:19:06: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:06: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:06: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:06: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:06: #2 predicted fragment length is 77 bps INFO @ Sat, 03 Apr 2021 06:19:06: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 03 Apr 2021 06:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.05_model.r WARNING @ Sat, 03 Apr 2021 06:19:06: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:19:06: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 03 Apr 2021 06:19:06: #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 06:19:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:19:08: 5000000 INFO @ Sat, 03 Apr 2021 06:19:10: 10000000 INFO @ Sat, 03 Apr 2021 06:19:14: 6000000 INFO @ Sat, 03 Apr 2021 06:19:17: 11000000 INFO @ Sat, 03 Apr 2021 06:19:21: 7000000 INFO @ Sat, 03 Apr 2021 06:19:24: 12000000 INFO @ Sat, 03 Apr 2021 06:19:28: 8000000 INFO @ Sat, 03 Apr 2021 06:19:30: 13000000 INFO @ Sat, 03 Apr 2021 06:19:34: 9000000 INFO @ Sat, 03 Apr 2021 06:19:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:19:36: 14000000 INFO @ Sat, 03 Apr 2021 06:19:37: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 06:19:37: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 06:19:37: #1 total tags in treatment: 14263953 INFO @ Sat, 03 Apr 2021 06:19:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:37: #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 06:19:38: #1 tags after filtering in treatment: 14263953 INFO @ Sat, 03 Apr 2021 06:19:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:19:38: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:19:39: #2 number of paired peaks: 1279 INFO @ Sat, 03 Apr 2021 06:19:39: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:39: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:39: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:39: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:39: #2 predicted fragment length is 77 bps INFO @ Sat, 03 Apr 2021 06:19:39: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 03 Apr 2021 06:19:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.10_model.r WARNING @ Sat, 03 Apr 2021 06:19:39: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:19:39: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 03 Apr 2021 06:19:39: #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 06:19:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:19:40: 10000000 INFO @ Sat, 03 Apr 2021 06:19:45: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.05_summits.bed INFO @ Sat, 03 Apr 2021 06:19:49: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (19999 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:19:51: 12000000 INFO @ Sat, 03 Apr 2021 06:19:57: 13000000 INFO @ Sat, 03 Apr 2021 06:20:02: 14000000 INFO @ Sat, 03 Apr 2021 06:20:04: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 06:20:04: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 06:20:04: #1 total tags in treatment: 14263953 INFO @ Sat, 03 Apr 2021 06:20:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:20:04: #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 06:20:04: #1 tags after filtering in treatment: 14263953 INFO @ Sat, 03 Apr 2021 06:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:20:04: #1 finished! INFO @ Sat, 03 Apr 2021 06:20:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:20:05: #2 number of paired peaks: 1279 INFO @ Sat, 03 Apr 2021 06:20:05: start model_add_line... INFO @ Sat, 03 Apr 2021 06:20:05: start X-correlation... INFO @ Sat, 03 Apr 2021 06:20:05: end of X-cor INFO @ Sat, 03 Apr 2021 06:20:05: #2 finished! INFO @ Sat, 03 Apr 2021 06:20:05: #2 predicted fragment length is 77 bps INFO @ Sat, 03 Apr 2021 06:20:05: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 03 Apr 2021 06:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.20_model.r WARNING @ Sat, 03 Apr 2021 06:20:05: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:20:05: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 03 Apr 2021 06:20:05: #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 06:20:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:20:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.10_summits.bed INFO @ Sat, 03 Apr 2021 06:20:20: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (14330 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:20:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:20:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:20:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:20:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082395/SRX4082395.20_summits.bed INFO @ Sat, 03 Apr 2021 06:20:46: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7932 records, 4 fields): 11 millis CompletedMACS2peakCalling