Job ID = 12264816 SRX = SRX7246273 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33208398 spots for SRR10564689/SRR10564689.sra Written 33208398 spots for SRR10564689/SRR10564689.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265635 ("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: 01:06:56 33208398 reads; of these: 33208398 (100.00%) were paired; of these: 22092278 (66.53%) aligned concordantly 0 times 9918222 (29.87%) aligned concordantly exactly 1 time 1197898 (3.61%) aligned concordantly >1 times ---- 22092278 pairs aligned concordantly 0 times; of these: 4823837 (21.83%) aligned discordantly 1 time ---- 17268441 pairs aligned 0 times concordantly or discordantly; of these: 34536882 mates make up the pairs; of these: 32786254 (94.93%) aligned 0 times 867917 (2.51%) aligned exactly 1 time 882711 (2.56%) aligned >1 times 50.64% overall alignment rate Time searching: 01:06:56 Overall time: 01:06:56 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 28 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 8455941 / 15814892 = 0.5347 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 07:42:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.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 07:42:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:42:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:42:14: 1000000 INFO @ Sat, 03 Apr 2021 07:42:24: 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 07:42:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.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 07:42:33: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:42:33: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:42:33: 3000000 INFO @ Sat, 03 Apr 2021 07:42:43: 4000000 INFO @ Sat, 03 Apr 2021 07:42:45: 1000000 INFO @ Sat, 03 Apr 2021 07:42:53: 5000000 INFO @ Sat, 03 Apr 2021 07:42:58: 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 07:43:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.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 07:43:03: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:43:03: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:43:04: 6000000 INFO @ Sat, 03 Apr 2021 07:43:12: 3000000 INFO @ Sat, 03 Apr 2021 07:43:15: 7000000 INFO @ Sat, 03 Apr 2021 07:43:18: 1000000 INFO @ Sat, 03 Apr 2021 07:43:25: 8000000 INFO @ Sat, 03 Apr 2021 07:43:26: 4000000 INFO @ Sat, 03 Apr 2021 07:43:32: 2000000 INFO @ Sat, 03 Apr 2021 07:43:37: 9000000 INFO @ Sat, 03 Apr 2021 07:43:40: 5000000 INFO @ Sat, 03 Apr 2021 07:43:46: 3000000 INFO @ Sat, 03 Apr 2021 07:43:48: 10000000 INFO @ Sat, 03 Apr 2021 07:43:54: 6000000 INFO @ Sat, 03 Apr 2021 07:43:59: 11000000 INFO @ Sat, 03 Apr 2021 07:44:01: 4000000 INFO @ Sat, 03 Apr 2021 07:44:07: 7000000 INFO @ Sat, 03 Apr 2021 07:44:10: 12000000 INFO @ Sat, 03 Apr 2021 07:44:15: 5000000 INFO @ Sat, 03 Apr 2021 07:44:20: 8000000 INFO @ Sat, 03 Apr 2021 07:44:20: 13000000 INFO @ Sat, 03 Apr 2021 07:44:29: 6000000 INFO @ Sat, 03 Apr 2021 07:44:33: 14000000 INFO @ Sat, 03 Apr 2021 07:44:34: 9000000 INFO @ Sat, 03 Apr 2021 07:44:43: 7000000 INFO @ Sat, 03 Apr 2021 07:44:47: 10000000 INFO @ Sat, 03 Apr 2021 07:44:49: 15000000 INFO @ Sat, 03 Apr 2021 07:44:56: 8000000 INFO @ Sat, 03 Apr 2021 07:44:59: 11000000 INFO @ Sat, 03 Apr 2021 07:44:59: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:45:07: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 07:45:07: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 07:45:07: #1 total tags in treatment: 4953405 INFO @ Sat, 03 Apr 2021 07:45:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:45:07: #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 07:45:07: #1 tags after filtering in treatment: 3751481 INFO @ Sat, 03 Apr 2021 07:45:07: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 07:45:07: #1 finished! INFO @ Sat, 03 Apr 2021 07:45:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:45:07: #2 number of paired peaks: 2272 INFO @ Sat, 03 Apr 2021 07:45:07: start model_add_line... INFO @ Sat, 03 Apr 2021 07:45:08: start X-correlation... INFO @ Sat, 03 Apr 2021 07:45:08: end of X-cor INFO @ Sat, 03 Apr 2021 07:45:08: #2 finished! INFO @ Sat, 03 Apr 2021 07:45:08: #2 predicted fragment length is 202 bps INFO @ Sat, 03 Apr 2021 07:45:08: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 03 Apr 2021 07:45:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.05_model.r WARNING @ Sat, 03 Apr 2021 07:45:08: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:45:08: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 03 Apr 2021 07:45:08: #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 07:45:08: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:45:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:45:10: 9000000 INFO @ Sat, 03 Apr 2021 07:45:12: 12000000 INFO @ Sat, 03 Apr 2021 07:45:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:45:23: 10000000 INFO @ Sat, 03 Apr 2021 07:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.05_summits.bed INFO @ Sat, 03 Apr 2021 07:45:23: Done! pass1 - making usageList (7 chroms): 15 millis pass2 - checking and writing primary data (4403 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:45:25: 13000000 INFO @ Sat, 03 Apr 2021 07:45:35: 11000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:45:37: 14000000 INFO @ Sat, 03 Apr 2021 07:45:47: 12000000 INFO @ Sat, 03 Apr 2021 07:45:49: 15000000 INFO @ Sat, 03 Apr 2021 07:46:00: 13000000 INFO @ Sat, 03 Apr 2021 07:46:02: 16000000 INFO @ Sat, 03 Apr 2021 07:46:10: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 07:46:10: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 07:46:10: #1 total tags in treatment: 4953405 INFO @ Sat, 03 Apr 2021 07:46:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:46:10: #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 07:46:11: #1 tags after filtering in treatment: 3751481 INFO @ Sat, 03 Apr 2021 07:46:11: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 07:46:11: #1 finished! INFO @ Sat, 03 Apr 2021 07:46:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:46:11: #2 number of paired peaks: 2272 INFO @ Sat, 03 Apr 2021 07:46:11: start model_add_line... INFO @ Sat, 03 Apr 2021 07:46:11: start X-correlation... INFO @ Sat, 03 Apr 2021 07:46:11: end of X-cor INFO @ Sat, 03 Apr 2021 07:46:11: #2 finished! INFO @ Sat, 03 Apr 2021 07:46:11: #2 predicted fragment length is 202 bps INFO @ Sat, 03 Apr 2021 07:46:11: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 03 Apr 2021 07:46:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.10_model.r WARNING @ Sat, 03 Apr 2021 07:46:11: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:46:11: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 03 Apr 2021 07:46:11: #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 07:46:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:46:12: 14000000 INFO @ Sat, 03 Apr 2021 07:46:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:46:24: 15000000 INFO @ Sat, 03 Apr 2021 07:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.10_summits.bed INFO @ Sat, 03 Apr 2021 07:46:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2637 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:46:34: 16000000 INFO @ Sat, 03 Apr 2021 07:46:42: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 07:46:42: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 07:46:42: #1 total tags in treatment: 4953405 INFO @ Sat, 03 Apr 2021 07:46:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:46:42: #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 07:46:42: #1 tags after filtering in treatment: 3751481 INFO @ Sat, 03 Apr 2021 07:46:42: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 07:46:42: #1 finished! INFO @ Sat, 03 Apr 2021 07:46:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:46:42: #2 number of paired peaks: 2272 INFO @ Sat, 03 Apr 2021 07:46:42: start model_add_line... INFO @ Sat, 03 Apr 2021 07:46:42: start X-correlation... INFO @ Sat, 03 Apr 2021 07:46:42: end of X-cor INFO @ Sat, 03 Apr 2021 07:46:42: #2 finished! INFO @ Sat, 03 Apr 2021 07:46:42: #2 predicted fragment length is 202 bps INFO @ Sat, 03 Apr 2021 07:46:42: #2 alternative fragment length(s) may be 202 bps INFO @ Sat, 03 Apr 2021 07:46:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.20_model.r WARNING @ Sat, 03 Apr 2021 07:46:42: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:46:42: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Sat, 03 Apr 2021 07:46:42: #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 07:46:42: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:46:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:46:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:46:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:46:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246273/SRX7246273.20_summits.bed INFO @ Sat, 03 Apr 2021 07:46:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1204 records, 4 fields): 4 millis CompletedMACS2peakCalling