Job ID = 14157954 SRX = SRX10641210 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19663986 spots for SRR14280068/SRR14280068.sra Written 19663986 spots for SRR14280068/SRR14280068.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158236 ("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: 00:24:47 19663986 reads; of these: 19663986 (100.00%) were paired; of these: 12847088 (65.33%) aligned concordantly 0 times 5718779 (29.08%) aligned concordantly exactly 1 time 1098119 (5.58%) aligned concordantly >1 times ---- 12847088 pairs aligned concordantly 0 times; of these: 3068762 (23.89%) aligned discordantly 1 time ---- 9778326 pairs aligned 0 times concordantly or discordantly; of these: 19556652 mates make up the pairs; of these: 18063295 (92.36%) aligned 0 times 812032 (4.15%) aligned exactly 1 time 681325 (3.48%) aligned >1 times 54.07% overall alignment rate Time searching: 00:24:47 Overall time: 00:24:47 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] 1444595 / 9855653 = 0.1466 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 13:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.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 13:53:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:53:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:53:29: 1000000 INFO @ Wed, 08 Dec 2021 13:53:38: 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 13:53:48: 3000000 INFO @ Wed, 08 Dec 2021 13:53:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.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 13:53:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:53:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:53:59: 1000000 INFO @ Wed, 08 Dec 2021 13:53:59: 4000000 INFO @ Wed, 08 Dec 2021 13:54:08: 2000000 INFO @ Wed, 08 Dec 2021 13:54:10: 5000000 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 13:54:18: 3000000 INFO @ Wed, 08 Dec 2021 13:54:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.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 13:54:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:54:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:54:22: 6000000 INFO @ Wed, 08 Dec 2021 13:54:28: 4000000 INFO @ Wed, 08 Dec 2021 13:54:29: 1000000 INFO @ Wed, 08 Dec 2021 13:54:33: 7000000 INFO @ Wed, 08 Dec 2021 13:54:39: 5000000 INFO @ Wed, 08 Dec 2021 13:54:40: 2000000 INFO @ Wed, 08 Dec 2021 13:54:45: 8000000 INFO @ Wed, 08 Dec 2021 13:54:49: 6000000 INFO @ Wed, 08 Dec 2021 13:54:50: 3000000 INFO @ Wed, 08 Dec 2021 13:54:56: 9000000 INFO @ Wed, 08 Dec 2021 13:55:00: 7000000 INFO @ Wed, 08 Dec 2021 13:55:00: 4000000 INFO @ Wed, 08 Dec 2021 13:55:07: 10000000 INFO @ Wed, 08 Dec 2021 13:55:10: 8000000 INFO @ Wed, 08 Dec 2021 13:55:11: 5000000 INFO @ Wed, 08 Dec 2021 13:55:18: 11000000 INFO @ Wed, 08 Dec 2021 13:55:20: 9000000 INFO @ Wed, 08 Dec 2021 13:55:21: 6000000 INFO @ Wed, 08 Dec 2021 13:55:29: 12000000 INFO @ Wed, 08 Dec 2021 13:55:31: 10000000 INFO @ Wed, 08 Dec 2021 13:55:31: 7000000 INFO @ Wed, 08 Dec 2021 13:55:40: 13000000 INFO @ Wed, 08 Dec 2021 13:55:41: 11000000 INFO @ Wed, 08 Dec 2021 13:55:42: 8000000 INFO @ Wed, 08 Dec 2021 13:55:51: 14000000 INFO @ Wed, 08 Dec 2021 13:55:51: 12000000 INFO @ Wed, 08 Dec 2021 13:55:52: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:56:02: 13000000 INFO @ Wed, 08 Dec 2021 13:56:02: 15000000 INFO @ Wed, 08 Dec 2021 13:56:02: 10000000 INFO @ Wed, 08 Dec 2021 13:56:12: 14000000 INFO @ Wed, 08 Dec 2021 13:56:13: 11000000 INFO @ Wed, 08 Dec 2021 13:56:13: 16000000 INFO @ Wed, 08 Dec 2021 13:56:22: 15000000 INFO @ Wed, 08 Dec 2021 13:56:23: 12000000 INFO @ Wed, 08 Dec 2021 13:56:24: 17000000 INFO @ Wed, 08 Dec 2021 13:56:33: 16000000 INFO @ Wed, 08 Dec 2021 13:56:33: 13000000 INFO @ Wed, 08 Dec 2021 13:56:35: 18000000 INFO @ Wed, 08 Dec 2021 13:56:39: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:56:39: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:56:39: #1 total tags in treatment: 5735355 INFO @ Wed, 08 Dec 2021 13:56:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:56:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:56:39: #1 tags after filtering in treatment: 5349455 INFO @ Wed, 08 Dec 2021 13:56:39: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:56:39: #1 finished! INFO @ Wed, 08 Dec 2021 13:56:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:56:39: #2 number of paired peaks: 581 WARNING @ Wed, 08 Dec 2021 13:56:39: Fewer paired peaks (581) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 581 pairs to build model! INFO @ Wed, 08 Dec 2021 13:56:39: start model_add_line... INFO @ Wed, 08 Dec 2021 13:56:39: start X-correlation... INFO @ Wed, 08 Dec 2021 13:56:39: end of X-cor INFO @ Wed, 08 Dec 2021 13:56:39: #2 finished! INFO @ Wed, 08 Dec 2021 13:56:39: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 13:56:39: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 13:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.05_model.r WARNING @ Wed, 08 Dec 2021 13:56:39: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:56:39: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 13:56:39: #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 13:56:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:56:43: 17000000 INFO @ Wed, 08 Dec 2021 13:56:43: 14000000 INFO @ Wed, 08 Dec 2021 13:56:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:56:52: 18000000 INFO @ Wed, 08 Dec 2021 13:56:53: 15000000 INFO @ Wed, 08 Dec 2021 13:56:56: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:56:56: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:56:56: #1 total tags in treatment: 5735355 INFO @ Wed, 08 Dec 2021 13:56:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:56:56: #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 13:56:56: #1 tags after filtering in treatment: 5349455 INFO @ Wed, 08 Dec 2021 13:56:56: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:56:56: #1 finished! INFO @ Wed, 08 Dec 2021 13:56:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:56:56: #2 number of paired peaks: 581 WARNING @ Wed, 08 Dec 2021 13:56:56: Fewer paired peaks (581) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 581 pairs to build model! INFO @ Wed, 08 Dec 2021 13:56:56: start model_add_line... INFO @ Wed, 08 Dec 2021 13:56:56: start X-correlation... INFO @ Wed, 08 Dec 2021 13:56:56: end of X-cor INFO @ Wed, 08 Dec 2021 13:56:56: #2 finished! INFO @ Wed, 08 Dec 2021 13:56:56: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 13:56:56: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 13:56:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.10_model.r WARNING @ Wed, 08 Dec 2021 13:56:56: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:56:56: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 13:56:56: #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 13:56:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:56:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.05_summits.bed INFO @ Wed, 08 Dec 2021 13:56:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (424 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:57:02: 16000000 INFO @ Wed, 08 Dec 2021 13:57:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:57:10: 17000000 INFO @ Wed, 08 Dec 2021 13:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.10_summits.bed INFO @ Wed, 08 Dec 2021 13:57:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:57:18: 18000000 INFO @ Wed, 08 Dec 2021 13:57:21: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:57:21: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:57:21: #1 total tags in treatment: 5735355 INFO @ Wed, 08 Dec 2021 13:57:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:57:21: #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 13:57:22: #1 tags after filtering in treatment: 5349455 INFO @ Wed, 08 Dec 2021 13:57:22: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:57:22: #1 finished! INFO @ Wed, 08 Dec 2021 13:57:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:57:22: #2 number of paired peaks: 581 WARNING @ Wed, 08 Dec 2021 13:57:22: Fewer paired peaks (581) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 581 pairs to build model! INFO @ Wed, 08 Dec 2021 13:57:22: start model_add_line... INFO @ Wed, 08 Dec 2021 13:57:22: start X-correlation... INFO @ Wed, 08 Dec 2021 13:57:22: end of X-cor INFO @ Wed, 08 Dec 2021 13:57:22: #2 finished! INFO @ Wed, 08 Dec 2021 13:57:22: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 13:57:22: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 13:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.20_model.r WARNING @ Wed, 08 Dec 2021 13:57:22: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:57:22: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 13:57:22: #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 13:57:22: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:57:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:57:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:57:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:57:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641210/SRX10641210.20_summits.bed INFO @ Wed, 08 Dec 2021 13:57:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis CompletedMACS2peakCalling