Job ID = 14157938 SRX = SRX10641208 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16812079 spots for SRR14280070/SRR14280070.sra Written 16812079 spots for SRR14280070/SRR14280070.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158210 ("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: 00:29:05 16812079 reads; of these: 16812079 (100.00%) were paired; of these: 8476033 (50.42%) aligned concordantly 0 times 7002823 (41.65%) aligned concordantly exactly 1 time 1333223 (7.93%) aligned concordantly >1 times ---- 8476033 pairs aligned concordantly 0 times; of these: 2675601 (31.57%) aligned discordantly 1 time ---- 5800432 pairs aligned 0 times concordantly or discordantly; of these: 11600864 mates make up the pairs; of these: 10454877 (90.12%) aligned 0 times 572409 (4.93%) aligned exactly 1 time 573578 (4.94%) aligned >1 times 68.91% overall alignment rate Time searching: 00:29:05 Overall time: 00:29:05 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_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] 1264317 / 10978414 = 0.1152 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 13:37:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.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 13:37:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:37:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:37:39: 1000000 INFO @ Wed, 08 Dec 2021 13:37:50: 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 13:37:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.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 13:37:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:37:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:37:59: 3000000 INFO @ Wed, 08 Dec 2021 13:38:09: 4000000 INFO @ Wed, 08 Dec 2021 13:38:10: 1000000 INFO @ Wed, 08 Dec 2021 13:38:19: 5000000 INFO @ Wed, 08 Dec 2021 13:38:22: 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 13:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.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 13:38:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:38:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:38:30: 6000000 INFO @ Wed, 08 Dec 2021 13:38:33: 3000000 INFO @ Wed, 08 Dec 2021 13:38:40: 1000000 INFO @ Wed, 08 Dec 2021 13:38:42: 7000000 INFO @ Wed, 08 Dec 2021 13:38:45: 4000000 INFO @ Wed, 08 Dec 2021 13:38:51: 2000000 INFO @ Wed, 08 Dec 2021 13:38:54: 8000000 INFO @ Wed, 08 Dec 2021 13:38:57: 5000000 INFO @ Wed, 08 Dec 2021 13:39:03: 3000000 INFO @ Wed, 08 Dec 2021 13:39:05: 9000000 INFO @ Wed, 08 Dec 2021 13:39:09: 6000000 INFO @ Wed, 08 Dec 2021 13:39:16: 4000000 INFO @ Wed, 08 Dec 2021 13:39:17: 10000000 INFO @ Wed, 08 Dec 2021 13:39:20: 7000000 INFO @ Wed, 08 Dec 2021 13:39:28: 5000000 INFO @ Wed, 08 Dec 2021 13:39:29: 11000000 INFO @ Wed, 08 Dec 2021 13:39:32: 8000000 INFO @ Wed, 08 Dec 2021 13:39:41: 6000000 INFO @ Wed, 08 Dec 2021 13:39:41: 12000000 INFO @ Wed, 08 Dec 2021 13:39:44: 9000000 INFO @ Wed, 08 Dec 2021 13:39:53: 13000000 INFO @ Wed, 08 Dec 2021 13:39:53: 7000000 INFO @ Wed, 08 Dec 2021 13:39:55: 10000000 INFO @ Wed, 08 Dec 2021 13:40:04: 14000000 INFO @ Wed, 08 Dec 2021 13:40:06: 8000000 INFO @ Wed, 08 Dec 2021 13:40:07: 11000000 INFO @ Wed, 08 Dec 2021 13:40:16: 15000000 INFO @ Wed, 08 Dec 2021 13:40:18: 9000000 INFO @ Wed, 08 Dec 2021 13:40:19: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:40:28: 16000000 INFO @ Wed, 08 Dec 2021 13:40:30: 10000000 INFO @ Wed, 08 Dec 2021 13:40:31: 13000000 INFO @ Wed, 08 Dec 2021 13:40:40: 17000000 INFO @ Wed, 08 Dec 2021 13:40:43: 14000000 INFO @ Wed, 08 Dec 2021 13:40:43: 11000000 INFO @ Wed, 08 Dec 2021 13:40:52: 18000000 INFO @ Wed, 08 Dec 2021 13:40:54: 15000000 INFO @ Wed, 08 Dec 2021 13:40:55: 12000000 INFO @ Wed, 08 Dec 2021 13:41:04: 19000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:41:06: 16000000 INFO @ Wed, 08 Dec 2021 13:41:08: 13000000 INFO @ Wed, 08 Dec 2021 13:41:16: 20000000 INFO @ Wed, 08 Dec 2021 13:41:18: 17000000 INFO @ Wed, 08 Dec 2021 13:41:20: 14000000 INFO @ Wed, 08 Dec 2021 13:41:24: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:41:24: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:41:24: #1 total tags in treatment: 7307894 INFO @ Wed, 08 Dec 2021 13:41:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:41:24: #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 13:41:25: #1 tags after filtering in treatment: 6792876 INFO @ Wed, 08 Dec 2021 13:41:25: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:41:25: #1 finished! INFO @ Wed, 08 Dec 2021 13:41:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:41:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:41:25: #2 number of paired peaks: 521 WARNING @ Wed, 08 Dec 2021 13:41:25: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Wed, 08 Dec 2021 13:41:25: start model_add_line... INFO @ Wed, 08 Dec 2021 13:41:25: start X-correlation... INFO @ Wed, 08 Dec 2021 13:41:25: end of X-cor INFO @ Wed, 08 Dec 2021 13:41:25: #2 finished! INFO @ Wed, 08 Dec 2021 13:41:25: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 13:41:25: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 13:41:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.05_model.r WARNING @ Wed, 08 Dec 2021 13:41:25: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:41:25: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 13:41:25: #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 13:41:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:41:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:41:29: 18000000 INFO @ Wed, 08 Dec 2021 13:41:33: 15000000 INFO @ Wed, 08 Dec 2021 13:41:40: 19000000 INFO @ Wed, 08 Dec 2021 13:41:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:41:45: 16000000 INFO @ Wed, 08 Dec 2021 13:41:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:41:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:41:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.05_summits.bed INFO @ Wed, 08 Dec 2021 13:41:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (463 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:41:52: 20000000 INFO @ Wed, 08 Dec 2021 13:41:58: 17000000 INFO @ Wed, 08 Dec 2021 13:41:59: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:41:59: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:41:59: #1 total tags in treatment: 7307894 INFO @ Wed, 08 Dec 2021 13:41:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:41:59: #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 13:41:59: #1 tags after filtering in treatment: 6792876 INFO @ Wed, 08 Dec 2021 13:41:59: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:41:59: #1 finished! INFO @ Wed, 08 Dec 2021 13:41:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:41:59: #2 number of paired peaks: 521 WARNING @ Wed, 08 Dec 2021 13:41:59: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Wed, 08 Dec 2021 13:41:59: start model_add_line... INFO @ Wed, 08 Dec 2021 13:42:00: start X-correlation... INFO @ Wed, 08 Dec 2021 13:42:00: end of X-cor INFO @ Wed, 08 Dec 2021 13:42:00: #2 finished! INFO @ Wed, 08 Dec 2021 13:42:00: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 13:42:00: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 13:42:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.10_model.r WARNING @ Wed, 08 Dec 2021 13:42:00: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:42:00: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 13:42:00: #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 13:42:00: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:42:09: 18000000 INFO @ Wed, 08 Dec 2021 13:42:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:42:20: 19000000 INFO @ Wed, 08 Dec 2021 13:42:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:42:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:42:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.10_summits.bed INFO @ Wed, 08 Dec 2021 13:42:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (354 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:42:31: 20000000 INFO @ Wed, 08 Dec 2021 13:42:37: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:42:37: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:42:37: #1 total tags in treatment: 7307894 INFO @ Wed, 08 Dec 2021 13:42:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:42:37: #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 13:42:38: #1 tags after filtering in treatment: 6792876 INFO @ Wed, 08 Dec 2021 13:42:38: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:42:38: #1 finished! INFO @ Wed, 08 Dec 2021 13:42:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:42:38: #2 number of paired peaks: 521 WARNING @ Wed, 08 Dec 2021 13:42:38: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Wed, 08 Dec 2021 13:42:38: start model_add_line... INFO @ Wed, 08 Dec 2021 13:42:38: start X-correlation... INFO @ Wed, 08 Dec 2021 13:42:38: end of X-cor INFO @ Wed, 08 Dec 2021 13:42:38: #2 finished! INFO @ Wed, 08 Dec 2021 13:42:38: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 13:42:38: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 13:42:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.20_model.r WARNING @ Wed, 08 Dec 2021 13:42:38: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:42:38: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 13:42:38: #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 13:42:38: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:42:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641208/SRX10641208.20_summits.bed INFO @ Wed, 08 Dec 2021 13:43:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 1 millis CompletedMACS2peakCalling