Job ID = 14157935 SRX = SRX10641205 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16473854 spots for SRR14280073/SRR14280073.sra Written 16473854 spots for SRR14280073/SRR14280073.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158224 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:36:11 16473854 reads; of these: 16473854 (100.00%) were paired; of these: 8740135 (53.05%) aligned concordantly 0 times 6761922 (41.05%) aligned concordantly exactly 1 time 971797 (5.90%) aligned concordantly >1 times ---- 8740135 pairs aligned concordantly 0 times; of these: 2475012 (28.32%) aligned discordantly 1 time ---- 6265123 pairs aligned 0 times concordantly or discordantly; of these: 12530246 mates make up the pairs; of these: 11467400 (91.52%) aligned 0 times 544131 (4.34%) aligned exactly 1 time 518715 (4.14%) aligned >1 times 65.20% overall alignment rate Time searching: 00:36:13 Overall time: 00:36:13 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] 1406395 / 10170617 = 0.1383 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 13:49:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.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 13:49:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:49:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:50:06: 1000000 INFO @ Wed, 08 Dec 2021 13:50:19: 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 13:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.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 13:50:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:50:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:50:32: 3000000 INFO @ Wed, 08 Dec 2021 13:50:34: 1000000 INFO @ Wed, 08 Dec 2021 13:50:44: 4000000 INFO @ Wed, 08 Dec 2021 13:50:44: 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 13:50:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.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 13:50:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:50:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:50:54: 3000000 INFO @ Wed, 08 Dec 2021 13:50:57: 5000000 INFO @ Wed, 08 Dec 2021 13:51:06: 4000000 INFO @ Wed, 08 Dec 2021 13:51:07: 1000000 INFO @ Wed, 08 Dec 2021 13:51:11: 6000000 INFO @ Wed, 08 Dec 2021 13:51:17: 5000000 INFO @ Wed, 08 Dec 2021 13:51:22: 2000000 INFO @ Wed, 08 Dec 2021 13:51:24: 7000000 INFO @ Wed, 08 Dec 2021 13:51:27: 6000000 INFO @ Wed, 08 Dec 2021 13:51:36: 3000000 INFO @ Wed, 08 Dec 2021 13:51:36: 7000000 INFO @ Wed, 08 Dec 2021 13:51:37: 8000000 INFO @ Wed, 08 Dec 2021 13:51:47: 8000000 INFO @ Wed, 08 Dec 2021 13:51:49: 4000000 INFO @ Wed, 08 Dec 2021 13:51:51: 9000000 INFO @ Wed, 08 Dec 2021 13:51:56: 9000000 INFO @ Wed, 08 Dec 2021 13:52:04: 5000000 INFO @ Wed, 08 Dec 2021 13:52:04: 10000000 INFO @ Wed, 08 Dec 2021 13:52:06: 10000000 INFO @ Wed, 08 Dec 2021 13:52:16: 11000000 INFO @ Wed, 08 Dec 2021 13:52:18: 11000000 INFO @ Wed, 08 Dec 2021 13:52:18: 6000000 INFO @ Wed, 08 Dec 2021 13:52:26: 12000000 INFO @ Wed, 08 Dec 2021 13:52:31: 12000000 INFO @ Wed, 08 Dec 2021 13:52:33: 7000000 INFO @ Wed, 08 Dec 2021 13:52:37: 13000000 INFO @ Wed, 08 Dec 2021 13:52:44: 13000000 INFO @ Wed, 08 Dec 2021 13:52:47: 8000000 INFO @ Wed, 08 Dec 2021 13:52:48: 14000000 INFO @ Wed, 08 Dec 2021 13:52:58: 14000000 INFO @ Wed, 08 Dec 2021 13:53:00: 15000000 INFO @ Wed, 08 Dec 2021 13:53:00: 9000000 INFO @ Wed, 08 Dec 2021 13:53:11: 15000000 INFO @ Wed, 08 Dec 2021 13:53:14: 10000000 INFO @ Wed, 08 Dec 2021 13:53:14: 16000000 INFO @ Wed, 08 Dec 2021 13:53:24: 16000000 INFO @ Wed, 08 Dec 2021 13:53:26: 17000000 INFO @ Wed, 08 Dec 2021 13:53:28: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:53:37: 18000000 INFO @ Wed, 08 Dec 2021 13:53:37: 17000000 INFO @ Wed, 08 Dec 2021 13:53:43: 12000000 INFO @ Wed, 08 Dec 2021 13:53:45: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:53:45: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:53:45: #1 total tags in treatment: 6591005 INFO @ Wed, 08 Dec 2021 13:53:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:53:45: #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 13:53:45: #1 tags after filtering in treatment: 6205022 INFO @ Wed, 08 Dec 2021 13:53:45: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 13:53:45: #1 finished! INFO @ Wed, 08 Dec 2021 13:53:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:53:45: #2 number of paired peaks: 399 WARNING @ Wed, 08 Dec 2021 13:53:45: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Wed, 08 Dec 2021 13:53:45: start model_add_line... INFO @ Wed, 08 Dec 2021 13:53:45: start X-correlation... INFO @ Wed, 08 Dec 2021 13:53:45: end of X-cor INFO @ Wed, 08 Dec 2021 13:53:45: #2 finished! INFO @ Wed, 08 Dec 2021 13:53:45: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 13:53:45: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 13:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.10_model.r WARNING @ Wed, 08 Dec 2021 13:53:45: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:53:45: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Wed, 08 Dec 2021 13:53:45: #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 13:53:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:53:50: 18000000 INFO @ Wed, 08 Dec 2021 13:53:57: 13000000 INFO @ Wed, 08 Dec 2021 13:53:59: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:53:59: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:53:59: #1 total tags in treatment: 6591005 INFO @ Wed, 08 Dec 2021 13:53:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:53:59: #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 13:53:59: #1 tags after filtering in treatment: 6205022 INFO @ Wed, 08 Dec 2021 13:53:59: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 13:53:59: #1 finished! INFO @ Wed, 08 Dec 2021 13:53:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:54:00: #2 number of paired peaks: 399 WARNING @ Wed, 08 Dec 2021 13:54:00: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Wed, 08 Dec 2021 13:54:00: start model_add_line... INFO @ Wed, 08 Dec 2021 13:54:00: start X-correlation... INFO @ Wed, 08 Dec 2021 13:54:00: end of X-cor INFO @ Wed, 08 Dec 2021 13:54:00: #2 finished! INFO @ Wed, 08 Dec 2021 13:54:00: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 13:54:00: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 13:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.05_model.r WARNING @ Wed, 08 Dec 2021 13:54:00: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:54:00: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Wed, 08 Dec 2021 13:54:00: #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 13:54:00: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:54:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:54:10: 14000000 INFO @ Wed, 08 Dec 2021 13:54:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:54:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:54:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.10_summits.bed INFO @ Wed, 08 Dec 2021 13:54:16: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (360 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:54:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:54:23: 15000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:54:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.05_summits.bed INFO @ Wed, 08 Dec 2021 13:54:32: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1335 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:54:37: 16000000 INFO @ Wed, 08 Dec 2021 13:54:51: 17000000 INFO @ Wed, 08 Dec 2021 13:55:04: 18000000 INFO @ Wed, 08 Dec 2021 13:55:13: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:55:13: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:55:13: #1 total tags in treatment: 6591005 INFO @ Wed, 08 Dec 2021 13:55:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:55:13: #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 13:55:13: #1 tags after filtering in treatment: 6205022 INFO @ Wed, 08 Dec 2021 13:55:13: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 13:55:13: #1 finished! INFO @ Wed, 08 Dec 2021 13:55:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:55:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:55:14: #2 number of paired peaks: 399 WARNING @ Wed, 08 Dec 2021 13:55:14: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Wed, 08 Dec 2021 13:55:14: start model_add_line... INFO @ Wed, 08 Dec 2021 13:55:14: start X-correlation... INFO @ Wed, 08 Dec 2021 13:55:14: end of X-cor INFO @ Wed, 08 Dec 2021 13:55:14: #2 finished! INFO @ Wed, 08 Dec 2021 13:55:14: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 13:55:14: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 13:55:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.20_model.r WARNING @ Wed, 08 Dec 2021 13:55:14: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:55:14: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Wed, 08 Dec 2021 13:55:14: #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 13:55:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:55:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:55:36: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:55:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:55:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:55:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641205/SRX10641205.20_summits.bed INFO @ Wed, 08 Dec 2021 13:55:46: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (185 records, 4 fields): 3 millis CompletedMACS2peakCalling