Job ID = 14158411 SRX = SRX10641194 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18841534 spots for SRR14280084/SRR14280084.sra Written 18841534 spots for SRR14280084/SRR14280084.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159192 ("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: 00:30:16 18841534 reads; of these: 18841534 (100.00%) were paired; of these: 11948475 (63.42%) aligned concordantly 0 times 4343476 (23.05%) aligned concordantly exactly 1 time 2549583 (13.53%) aligned concordantly >1 times ---- 11948475 pairs aligned concordantly 0 times; of these: 1669590 (13.97%) aligned discordantly 1 time ---- 10278885 pairs aligned 0 times concordantly or discordantly; of these: 20557770 mates make up the pairs; of these: 19726588 (95.96%) aligned 0 times 421048 (2.05%) aligned exactly 1 time 410134 (2.00%) aligned >1 times 47.65% overall alignment rate Time searching: 00:30:16 Overall time: 00:30:16 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_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] 1667821 / 8523866 = 0.1957 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 @ Wed, 08 Dec 2021 18:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.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 @ Wed, 08 Dec 2021 18:12:06: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:12:06: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:12:16: 1000000 INFO @ Wed, 08 Dec 2021 18:12:25: 2000000 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 @ Wed, 08 Dec 2021 18:12:34: 3000000 INFO @ Wed, 08 Dec 2021 18:12:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.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 @ Wed, 08 Dec 2021 18:12:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:12:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:12:45: 4000000 INFO @ Wed, 08 Dec 2021 18:12:46: 1000000 INFO @ Wed, 08 Dec 2021 18:12:57: 5000000 INFO @ Wed, 08 Dec 2021 18:12:58: 2000000 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 @ Wed, 08 Dec 2021 18:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.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 @ Wed, 08 Dec 2021 18:13:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:13:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:13:08: 6000000 INFO @ Wed, 08 Dec 2021 18:13:10: 3000000 INFO @ Wed, 08 Dec 2021 18:13:15: 1000000 INFO @ Wed, 08 Dec 2021 18:13:20: 7000000 INFO @ Wed, 08 Dec 2021 18:13:21: 4000000 INFO @ Wed, 08 Dec 2021 18:13:26: 2000000 INFO @ Wed, 08 Dec 2021 18:13:32: 5000000 INFO @ Wed, 08 Dec 2021 18:13:32: 8000000 INFO @ Wed, 08 Dec 2021 18:13:36: 3000000 INFO @ Wed, 08 Dec 2021 18:13:43: 6000000 INFO @ Wed, 08 Dec 2021 18:13:44: 9000000 INFO @ Wed, 08 Dec 2021 18:13:48: 4000000 INFO @ Wed, 08 Dec 2021 18:13:53: 7000000 INFO @ Wed, 08 Dec 2021 18:13:57: 10000000 INFO @ Wed, 08 Dec 2021 18:14:00: 5000000 INFO @ Wed, 08 Dec 2021 18:14:04: 8000000 INFO @ Wed, 08 Dec 2021 18:14:09: 11000000 INFO @ Wed, 08 Dec 2021 18:14:12: 6000000 INFO @ Wed, 08 Dec 2021 18:14:14: 9000000 INFO @ Wed, 08 Dec 2021 18:14:21: 12000000 INFO @ Wed, 08 Dec 2021 18:14:23: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:14:25: 10000000 INFO @ Wed, 08 Dec 2021 18:14:33: 13000000 INFO @ Wed, 08 Dec 2021 18:14:35: 8000000 INFO @ Wed, 08 Dec 2021 18:14:35: 11000000 INFO @ Wed, 08 Dec 2021 18:14:45: 14000000 INFO @ Wed, 08 Dec 2021 18:14:46: 12000000 INFO @ Wed, 08 Dec 2021 18:14:47: 9000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:14:52: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:14:52: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:14:52: #1 total tags in treatment: 5390325 INFO @ Wed, 08 Dec 2021 18:14:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:14:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:14:52: #1 tags after filtering in treatment: 4160602 INFO @ Wed, 08 Dec 2021 18:14:52: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 18:14:52: #1 finished! INFO @ Wed, 08 Dec 2021 18:14:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:14:53: #2 number of paired peaks: 1248 INFO @ Wed, 08 Dec 2021 18:14:53: start model_add_line... INFO @ Wed, 08 Dec 2021 18:14:53: start X-correlation... INFO @ Wed, 08 Dec 2021 18:14:53: end of X-cor INFO @ Wed, 08 Dec 2021 18:14:53: #2 finished! INFO @ Wed, 08 Dec 2021 18:14:53: #2 predicted fragment length is 263 bps INFO @ Wed, 08 Dec 2021 18:14:53: #2 alternative fragment length(s) may be 263 bps INFO @ Wed, 08 Dec 2021 18:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.05_model.r WARNING @ Wed, 08 Dec 2021 18:14:53: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:14:53: #2 You may need to consider one of the other alternative d(s): 263 WARNING @ Wed, 08 Dec 2021 18:14:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 18:14:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:14:56: 13000000 INFO @ Wed, 08 Dec 2021 18:14:59: 10000000 INFO @ Wed, 08 Dec 2021 18:15:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:15:06: 14000000 INFO @ Wed, 08 Dec 2021 18:15:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:15:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:15:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.05_summits.bed INFO @ Wed, 08 Dec 2021 18:15:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2352 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:15:11: 11000000 INFO @ Wed, 08 Dec 2021 18:15:13: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:15:13: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:15:13: #1 total tags in treatment: 5390325 INFO @ Wed, 08 Dec 2021 18:15:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:15:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:15:13: #1 tags after filtering in treatment: 4160602 INFO @ Wed, 08 Dec 2021 18:15:13: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 18:15:13: #1 finished! INFO @ Wed, 08 Dec 2021 18:15:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:15:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:15:13: #2 number of paired peaks: 1248 INFO @ Wed, 08 Dec 2021 18:15:13: start model_add_line... INFO @ Wed, 08 Dec 2021 18:15:13: start X-correlation... INFO @ Wed, 08 Dec 2021 18:15:13: end of X-cor INFO @ Wed, 08 Dec 2021 18:15:13: #2 finished! INFO @ Wed, 08 Dec 2021 18:15:13: #2 predicted fragment length is 263 bps INFO @ Wed, 08 Dec 2021 18:15:13: #2 alternative fragment length(s) may be 263 bps INFO @ Wed, 08 Dec 2021 18:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.10_model.r WARNING @ Wed, 08 Dec 2021 18:15:13: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:15:13: #2 You may need to consider one of the other alternative d(s): 263 WARNING @ Wed, 08 Dec 2021 18:15:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 18:15:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:15:22: 12000000 INFO @ Wed, 08 Dec 2021 18:15:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.10_summits.bed INFO @ Wed, 08 Dec 2021 18:15:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1247 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:15:32: 13000000 INFO @ Wed, 08 Dec 2021 18:15:43: 14000000 INFO @ Wed, 08 Dec 2021 18:15:49: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:15:49: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:15:49: #1 total tags in treatment: 5390325 INFO @ Wed, 08 Dec 2021 18:15:49: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:15:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:15:49: #1 tags after filtering in treatment: 4160602 INFO @ Wed, 08 Dec 2021 18:15:49: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 18:15:49: #1 finished! INFO @ Wed, 08 Dec 2021 18:15:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:15:50: #2 number of paired peaks: 1248 INFO @ Wed, 08 Dec 2021 18:15:50: start model_add_line... INFO @ Wed, 08 Dec 2021 18:15:50: start X-correlation... INFO @ Wed, 08 Dec 2021 18:15:50: end of X-cor INFO @ Wed, 08 Dec 2021 18:15:50: #2 finished! INFO @ Wed, 08 Dec 2021 18:15:50: #2 predicted fragment length is 263 bps INFO @ Wed, 08 Dec 2021 18:15:50: #2 alternative fragment length(s) may be 263 bps INFO @ Wed, 08 Dec 2021 18:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.20_model.r WARNING @ Wed, 08 Dec 2021 18:15:50: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:15:50: #2 You may need to consider one of the other alternative d(s): 263 WARNING @ Wed, 08 Dec 2021 18:15:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 18:15:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:16:01: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:16:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:16:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:16:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641194/SRX10641194.20_summits.bed INFO @ Wed, 08 Dec 2021 18:16:06: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (618 records, 4 fields): 2 millis CompletedMACS2peakCalling