Job ID = 14160338 SRX = SRX9567167 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30931526 spots for SRR13125142/SRR13125142.sra Written 30931526 spots for SRR13125142/SRR13125142.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160778 ("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: 02:04:31 30931526 reads; of these: 30931526 (100.00%) were paired; of these: 13393744 (43.30%) aligned concordantly 0 times 9483949 (30.66%) aligned concordantly exactly 1 time 8053833 (26.04%) aligned concordantly >1 times ---- 13393744 pairs aligned concordantly 0 times; of these: 6283870 (46.92%) aligned discordantly 1 time ---- 7109874 pairs aligned 0 times concordantly or discordantly; of these: 14219748 mates make up the pairs; of these: 11042012 (77.65%) aligned 0 times 1360206 (9.57%) aligned exactly 1 time 1817530 (12.78%) aligned >1 times 82.15% overall alignment rate Time searching: 02:04:31 Overall time: 02:04:31 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 40 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] 19778788 / 23788984 = 0.8314 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.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 @ Thu, 09 Dec 2021 03:59:21: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:59:21: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:59:37: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.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 @ Thu, 09 Dec 2021 03:59:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:59:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:59:52: 2000000 INFO @ Thu, 09 Dec 2021 04:00:05: 1000000 INFO @ Thu, 09 Dec 2021 04:00:07: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:00:18: 2000000 INFO @ Thu, 09 Dec 2021 04:00:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.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 @ Thu, 09 Dec 2021 04:00:21: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:00:21: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:00:23: 4000000 INFO @ Thu, 09 Dec 2021 04:00:33: 3000000 INFO @ Thu, 09 Dec 2021 04:00:36: 1000000 INFO @ Thu, 09 Dec 2021 04:00:38: 5000000 INFO @ Thu, 09 Dec 2021 04:00:46: 4000000 INFO @ Thu, 09 Dec 2021 04:00:50: 2000000 INFO @ Thu, 09 Dec 2021 04:00:54: 6000000 INFO @ Thu, 09 Dec 2021 04:01:00: 5000000 INFO @ Thu, 09 Dec 2021 04:01:05: 3000000 INFO @ Thu, 09 Dec 2021 04:01:09: 7000000 INFO @ Thu, 09 Dec 2021 04:01:14: 6000000 INFO @ Thu, 09 Dec 2021 04:01:19: 4000000 INFO @ Thu, 09 Dec 2021 04:01:24: 8000000 INFO @ Thu, 09 Dec 2021 04:01:29: 7000000 INFO @ Thu, 09 Dec 2021 04:01:33: 5000000 INFO @ Thu, 09 Dec 2021 04:01:39: 9000000 INFO @ Thu, 09 Dec 2021 04:01:43: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:01:46: 6000000 INFO @ Thu, 09 Dec 2021 04:01:54: 10000000 INFO @ Thu, 09 Dec 2021 04:01:56: 9000000 INFO @ Thu, 09 Dec 2021 04:02:00: 7000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:02:09: 11000000 INFO @ Thu, 09 Dec 2021 04:02:09: 10000000 INFO @ Thu, 09 Dec 2021 04:02:13: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:02:13: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:02:13: #1 total tags in treatment: 3048321 INFO @ Thu, 09 Dec 2021 04:02:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:02:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:02:13: #1 tags after filtering in treatment: 1894640 INFO @ Thu, 09 Dec 2021 04:02:13: #1 Redundant rate of treatment: 0.38 INFO @ Thu, 09 Dec 2021 04:02:13: #1 finished! INFO @ Thu, 09 Dec 2021 04:02:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:02:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:02:13: #2 number of paired peaks: 1187 INFO @ Thu, 09 Dec 2021 04:02:13: start model_add_line... INFO @ Thu, 09 Dec 2021 04:02:13: start X-correlation... INFO @ Thu, 09 Dec 2021 04:02:13: end of X-cor INFO @ Thu, 09 Dec 2021 04:02:13: #2 finished! INFO @ Thu, 09 Dec 2021 04:02:13: #2 predicted fragment length is 291 bps INFO @ Thu, 09 Dec 2021 04:02:13: #2 alternative fragment length(s) may be 291 bps INFO @ Thu, 09 Dec 2021 04:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.05_model.r WARNING @ Thu, 09 Dec 2021 04:02:13: #2 Since the d (291) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:02:13: #2 You may need to consider one of the other alternative d(s): 291 WARNING @ Thu, 09 Dec 2021 04:02:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:02:13: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:02:14: 8000000 INFO @ Thu, 09 Dec 2021 04:02:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:02:22: 11000000 INFO @ Thu, 09 Dec 2021 04:02:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:02:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:02:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.05_summits.bed INFO @ Thu, 09 Dec 2021 04:02:25: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (960 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:02:25: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:02:25: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:02:25: #1 total tags in treatment: 3048321 INFO @ Thu, 09 Dec 2021 04:02:25: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:02:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:02:25: #1 tags after filtering in treatment: 1894640 INFO @ Thu, 09 Dec 2021 04:02:25: #1 Redundant rate of treatment: 0.38 INFO @ Thu, 09 Dec 2021 04:02:25: #1 finished! INFO @ Thu, 09 Dec 2021 04:02:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:02:26: #2 number of paired peaks: 1187 INFO @ Thu, 09 Dec 2021 04:02:26: start model_add_line... INFO @ Thu, 09 Dec 2021 04:02:26: start X-correlation... INFO @ Thu, 09 Dec 2021 04:02:26: end of X-cor INFO @ Thu, 09 Dec 2021 04:02:26: #2 finished! INFO @ Thu, 09 Dec 2021 04:02:26: #2 predicted fragment length is 291 bps INFO @ Thu, 09 Dec 2021 04:02:26: #2 alternative fragment length(s) may be 291 bps INFO @ Thu, 09 Dec 2021 04:02:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.10_model.r WARNING @ Thu, 09 Dec 2021 04:02:26: #2 Since the d (291) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:02:26: #2 You may need to consider one of the other alternative d(s): 291 WARNING @ Thu, 09 Dec 2021 04:02:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:02:26: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:02:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:02:27: 9000000 INFO @ Thu, 09 Dec 2021 04:02:34: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:02:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:02:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:02:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.10_summits.bed INFO @ Thu, 09 Dec 2021 04:02:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (648 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:02:38: 10000000 INFO @ Thu, 09 Dec 2021 04:02:50: 11000000 INFO @ Thu, 09 Dec 2021 04:02:53: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:02:53: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:02:53: #1 total tags in treatment: 3048321 INFO @ Thu, 09 Dec 2021 04:02:53: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:02:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:02:53: #1 tags after filtering in treatment: 1894640 INFO @ Thu, 09 Dec 2021 04:02:53: #1 Redundant rate of treatment: 0.38 INFO @ Thu, 09 Dec 2021 04:02:53: #1 finished! INFO @ Thu, 09 Dec 2021 04:02:53: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:02:53: #2 number of paired peaks: 1187 INFO @ Thu, 09 Dec 2021 04:02:53: start model_add_line... INFO @ Thu, 09 Dec 2021 04:02:53: start X-correlation... INFO @ Thu, 09 Dec 2021 04:02:53: end of X-cor INFO @ Thu, 09 Dec 2021 04:02:53: #2 finished! INFO @ Thu, 09 Dec 2021 04:02:53: #2 predicted fragment length is 291 bps INFO @ Thu, 09 Dec 2021 04:02:53: #2 alternative fragment length(s) may be 291 bps INFO @ Thu, 09 Dec 2021 04:02:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.20_model.r WARNING @ Thu, 09 Dec 2021 04:02:53: #2 Since the d (291) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:02:53: #2 You may need to consider one of the other alternative d(s): 291 WARNING @ Thu, 09 Dec 2021 04:02:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:02:53: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:02:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:03:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:03:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:03:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:03:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567167/SRX9567167.20_summits.bed INFO @ Thu, 09 Dec 2021 04:03:05: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (462 records, 4 fields): 4 millis CompletedMACS2peakCalling