Job ID = 14157937 SRX = SRX10641207 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18394539 spots for SRR14280071/SRR14280071.sra Written 18394539 spots for SRR14280071/SRR14280071.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158231 ("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: 00:39:50 18394539 reads; of these: 18394539 (100.00%) were paired; of these: 10365533 (56.35%) aligned concordantly 0 times 6853799 (37.26%) aligned concordantly exactly 1 time 1175207 (6.39%) aligned concordantly >1 times ---- 10365533 pairs aligned concordantly 0 times; of these: 3070890 (29.63%) aligned discordantly 1 time ---- 7294643 pairs aligned 0 times concordantly or discordantly; of these: 14589286 mates make up the pairs; of these: 13164403 (90.23%) aligned 0 times 779788 (5.34%) aligned exactly 1 time 645095 (4.42%) aligned >1 times 64.22% overall alignment rate Time searching: 00:39:50 Overall time: 00:39:50 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] 1552482 / 11066342 = 0.1403 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 13:55:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.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 13:55:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:55:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:55:55: 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 @ Wed, 08 Dec 2021 13:56:09: 2000000 INFO @ Wed, 08 Dec 2021 13:56:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.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 13:56:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:56:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:56:25: 1000000 INFO @ Wed, 08 Dec 2021 13:56:25: 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 @ Wed, 08 Dec 2021 13:56:39: 2000000 INFO @ Wed, 08 Dec 2021 13:56:39: 4000000 INFO @ Wed, 08 Dec 2021 13:56:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.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 13:56:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:56:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:56:53: 3000000 INFO @ Wed, 08 Dec 2021 13:56:53: 1000000 INFO @ Wed, 08 Dec 2021 13:56:55: 5000000 INFO @ Wed, 08 Dec 2021 13:57:06: 2000000 INFO @ Wed, 08 Dec 2021 13:57:07: 4000000 INFO @ Wed, 08 Dec 2021 13:57:11: 6000000 INFO @ Wed, 08 Dec 2021 13:57:20: 3000000 INFO @ Wed, 08 Dec 2021 13:57:21: 5000000 INFO @ Wed, 08 Dec 2021 13:57:25: 7000000 INFO @ Wed, 08 Dec 2021 13:57:32: 4000000 INFO @ Wed, 08 Dec 2021 13:57:36: 6000000 INFO @ Wed, 08 Dec 2021 13:57:41: 8000000 INFO @ Wed, 08 Dec 2021 13:57:44: 5000000 INFO @ Wed, 08 Dec 2021 13:57:50: 7000000 INFO @ Wed, 08 Dec 2021 13:57:57: 9000000 INFO @ Wed, 08 Dec 2021 13:57:57: 6000000 INFO @ Wed, 08 Dec 2021 13:58:05: 8000000 INFO @ Wed, 08 Dec 2021 13:58:10: 7000000 INFO @ Wed, 08 Dec 2021 13:58:12: 10000000 INFO @ Wed, 08 Dec 2021 13:58:19: 9000000 INFO @ Wed, 08 Dec 2021 13:58:22: 8000000 INFO @ Wed, 08 Dec 2021 13:58:27: 11000000 INFO @ Wed, 08 Dec 2021 13:58:33: 10000000 INFO @ Wed, 08 Dec 2021 13:58:35: 9000000 INFO @ Wed, 08 Dec 2021 13:58:41: 12000000 INFO @ Wed, 08 Dec 2021 13:58:47: 10000000 INFO @ Wed, 08 Dec 2021 13:58:47: 11000000 INFO @ Wed, 08 Dec 2021 13:58:55: 13000000 INFO @ Wed, 08 Dec 2021 13:58:59: 11000000 INFO @ Wed, 08 Dec 2021 13:59:01: 12000000 INFO @ Wed, 08 Dec 2021 13:59:09: 14000000 INFO @ Wed, 08 Dec 2021 13:59:11: 12000000 INFO @ Wed, 08 Dec 2021 13:59:14: 13000000 INFO @ Wed, 08 Dec 2021 13:59:23: 13000000 INFO @ Wed, 08 Dec 2021 13:59:24: 15000000 INFO @ Wed, 08 Dec 2021 13:59:27: 14000000 INFO @ Wed, 08 Dec 2021 13:59:35: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:59:38: 16000000 INFO @ Wed, 08 Dec 2021 13:59:41: 15000000 INFO @ Wed, 08 Dec 2021 13:59:47: 15000000 INFO @ Wed, 08 Dec 2021 13:59:52: 17000000 INFO @ Wed, 08 Dec 2021 13:59:54: 16000000 INFO @ Wed, 08 Dec 2021 13:59:59: 16000000 INFO @ Wed, 08 Dec 2021 14:00:06: 18000000 INFO @ Wed, 08 Dec 2021 14:00:08: 17000000 INFO @ Wed, 08 Dec 2021 14:00:11: 17000000 INFO @ Wed, 08 Dec 2021 14:00:20: 19000000 INFO @ Wed, 08 Dec 2021 14:00:22: 18000000 INFO @ Wed, 08 Dec 2021 14:00:23: 18000000 INFO @ Wed, 08 Dec 2021 14:00:35: 20000000 INFO @ Wed, 08 Dec 2021 14:00:35: 19000000 INFO @ Wed, 08 Dec 2021 14:00:36: 19000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:00:42: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:00:42: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:00:42: #1 total tags in treatment: 6819793 INFO @ Wed, 08 Dec 2021 14:00:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:00:42: #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 14:00:43: #1 tags after filtering in treatment: 6401746 INFO @ Wed, 08 Dec 2021 14:00:43: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 14:00:43: #1 finished! INFO @ Wed, 08 Dec 2021 14:00:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:00:43: #2 number of paired peaks: 474 WARNING @ Wed, 08 Dec 2021 14:00:43: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Wed, 08 Dec 2021 14:00:43: start model_add_line... INFO @ Wed, 08 Dec 2021 14:00:43: start X-correlation... INFO @ Wed, 08 Dec 2021 14:00:43: end of X-cor INFO @ Wed, 08 Dec 2021 14:00:43: #2 finished! INFO @ Wed, 08 Dec 2021 14:00:43: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 14:00:43: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 14:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.05_model.r WARNING @ Wed, 08 Dec 2021 14:00:43: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:00:43: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 14:00:43: #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 14:00:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:00:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:00:47: 20000000 INFO @ Wed, 08 Dec 2021 14:00:50: 20000000 INFO @ Wed, 08 Dec 2021 14:00:53: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:00:53: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:00:53: #1 total tags in treatment: 6819793 INFO @ Wed, 08 Dec 2021 14:00:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:00:53: #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 14:00:53: #1 tags after filtering in treatment: 6401746 INFO @ Wed, 08 Dec 2021 14:00:53: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 14:00:53: #1 finished! INFO @ Wed, 08 Dec 2021 14:00:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:00:54: #2 number of paired peaks: 474 WARNING @ Wed, 08 Dec 2021 14:00:54: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Wed, 08 Dec 2021 14:00:54: start model_add_line... INFO @ Wed, 08 Dec 2021 14:00:54: start X-correlation... INFO @ Wed, 08 Dec 2021 14:00:54: end of X-cor INFO @ Wed, 08 Dec 2021 14:00:54: #2 finished! INFO @ Wed, 08 Dec 2021 14:00:54: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 14:00:54: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 14:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.20_model.r WARNING @ Wed, 08 Dec 2021 14:00:54: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:00:54: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 14:00:54: #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 14:00:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:00:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:00:57: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:00:57: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:00:57: #1 total tags in treatment: 6819793 INFO @ Wed, 08 Dec 2021 14:00:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:00:57: #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 14:00:57: #1 tags after filtering in treatment: 6401746 INFO @ Wed, 08 Dec 2021 14:00:57: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 14:00:57: #1 finished! INFO @ Wed, 08 Dec 2021 14:00:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:00:58: #2 number of paired peaks: 474 WARNING @ Wed, 08 Dec 2021 14:00:58: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Wed, 08 Dec 2021 14:00:58: start model_add_line... INFO @ Wed, 08 Dec 2021 14:00:58: start X-correlation... INFO @ Wed, 08 Dec 2021 14:00:58: end of X-cor INFO @ Wed, 08 Dec 2021 14:00:58: #2 finished! INFO @ Wed, 08 Dec 2021 14:00:58: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 14:00:58: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 14:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.10_model.r WARNING @ Wed, 08 Dec 2021 14:00:58: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:00:58: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 14:00:58: #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 14:00:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:01:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:01:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:01:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:01:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.05_summits.bed INFO @ Wed, 08 Dec 2021 14:01:15: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (530 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:01:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:01:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:01:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.20_summits.bed INFO @ Wed, 08 Dec 2021 14:01:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:01:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:01:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:01:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641207/SRX10641207.10_summits.bed INFO @ Wed, 08 Dec 2021 14:01:31: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (327 records, 4 fields): 6 millis CompletedMACS2peakCalling