Job ID = 12264812 SRX = SRX7246269 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23264534 spots for SRR10564683/SRR10564683.sra Written 23264534 spots for SRR10564683/SRR10564683.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265500 ("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: 00:52:53 23264534 reads; of these: 23264534 (100.00%) were paired; of these: 11541763 (49.61%) aligned concordantly 0 times 9801398 (42.13%) aligned concordantly exactly 1 time 1921373 (8.26%) aligned concordantly >1 times ---- 11541763 pairs aligned concordantly 0 times; of these: 3171789 (27.48%) aligned discordantly 1 time ---- 8369974 pairs aligned 0 times concordantly or discordantly; of these: 16739948 mates make up the pairs; of these: 15115913 (90.30%) aligned 0 times 551513 (3.29%) aligned exactly 1 time 1072522 (6.41%) aligned >1 times 67.51% overall alignment rate Time searching: 00:52:53 Overall time: 00:52:53 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 24 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] 3978063 / 14794862 = 0.2689 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.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 @ Sat, 03 Apr 2021 07:07:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:07:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:38: 1000000 INFO @ Sat, 03 Apr 2021 07:07:49: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:07:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.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 @ Sat, 03 Apr 2021 07:07:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:07:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:08:01: 3000000 INFO @ Sat, 03 Apr 2021 07:08:08: 1000000 INFO @ Sat, 03 Apr 2021 07:08:13: 4000000 BedGraph に変換中... INFO @ Sat, 03 Apr 2021 07:08:21: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:08:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.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 @ Sat, 03 Apr 2021 07:08:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:08:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:08:26: 5000000 INFO @ Sat, 03 Apr 2021 07:08:34: 3000000 INFO @ Sat, 03 Apr 2021 07:08:39: 6000000 INFO @ Sat, 03 Apr 2021 07:08:41: 1000000 INFO @ Sat, 03 Apr 2021 07:08:46: 4000000 INFO @ Sat, 03 Apr 2021 07:08:52: 7000000 INFO @ Sat, 03 Apr 2021 07:08:53: 2000000 INFO @ Sat, 03 Apr 2021 07:08:59: 5000000 INFO @ Sat, 03 Apr 2021 07:09:05: 8000000 INFO @ Sat, 03 Apr 2021 07:09:05: 3000000 INFO @ Sat, 03 Apr 2021 07:09:14: 6000000 INFO @ Sat, 03 Apr 2021 07:09:18: 4000000 INFO @ Sat, 03 Apr 2021 07:09:18: 9000000 INFO @ Sat, 03 Apr 2021 07:09:30: 5000000 INFO @ Sat, 03 Apr 2021 07:09:31: 7000000 INFO @ Sat, 03 Apr 2021 07:09:31: 10000000 INFO @ Sat, 03 Apr 2021 07:09:43: 6000000 INFO @ Sat, 03 Apr 2021 07:09:44: 11000000 INFO @ Sat, 03 Apr 2021 07:09:48: 8000000 INFO @ Sat, 03 Apr 2021 07:09:55: 7000000 INFO @ Sat, 03 Apr 2021 07:09:58: 12000000 INFO @ Sat, 03 Apr 2021 07:10:00: 9000000 INFO @ Sat, 03 Apr 2021 07:10:08: 8000000 INFO @ Sat, 03 Apr 2021 07:10:12: 13000000 INFO @ Sat, 03 Apr 2021 07:10:16: 10000000 INFO @ Sat, 03 Apr 2021 07:10:21: 9000000 INFO @ Sat, 03 Apr 2021 07:10:25: 14000000 INFO @ Sat, 03 Apr 2021 07:10:29: 11000000 INFO @ Sat, 03 Apr 2021 07:10:34: 10000000 INFO @ Sat, 03 Apr 2021 07:10:39: 15000000 INFO @ Sat, 03 Apr 2021 07:10:44: 12000000 INFO @ Sat, 03 Apr 2021 07:10:48: 11000000 INFO @ Sat, 03 Apr 2021 07:10:52: 16000000 INFO @ Sat, 03 Apr 2021 07:10:58: 13000000 INFO @ Sat, 03 Apr 2021 07:11:03: 12000000 INFO @ Sat, 03 Apr 2021 07:11:05: 17000000 INFO @ Sat, 03 Apr 2021 07:11:13: 14000000 INFO @ Sat, 03 Apr 2021 07:11:17: 13000000 INFO @ Sat, 03 Apr 2021 07:11:19: 18000000 INFO @ Sat, 03 Apr 2021 07:11:26: 15000000 INFO @ Sat, 03 Apr 2021 07:11:30: 14000000 INFO @ Sat, 03 Apr 2021 07:11:32: 19000000 INFO @ Sat, 03 Apr 2021 07:11:38: 16000000 INFO @ Sat, 03 Apr 2021 07:11:43: 15000000 INFO @ Sat, 03 Apr 2021 07:11:45: 20000000 INFO @ Sat, 03 Apr 2021 07:11:50: 17000000 INFO @ Sat, 03 Apr 2021 07:11:55: 16000000 INFO @ Sat, 03 Apr 2021 07:11:58: 21000000 INFO @ Sat, 03 Apr 2021 07:12:03: 18000000 INFO @ Sat, 03 Apr 2021 07:12:09: 17000000 INFO @ Sat, 03 Apr 2021 07:12:11: 22000000 INFO @ Sat, 03 Apr 2021 07:12:16: 19000000 INFO @ Sat, 03 Apr 2021 07:12:21: 18000000 INFO @ Sat, 03 Apr 2021 07:12:23: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:12:28: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 07:12:28: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 07:12:28: #1 total tags in treatment: 8465678 INFO @ Sat, 03 Apr 2021 07:12:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:12:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:12:29: #1 tags after filtering in treatment: 6331798 INFO @ Sat, 03 Apr 2021 07:12:29: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:12:29: #1 finished! INFO @ Sat, 03 Apr 2021 07:12:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:12:29: 20000000 INFO @ Sat, 03 Apr 2021 07:12:29: #2 number of paired peaks: 958 WARNING @ Sat, 03 Apr 2021 07:12:29: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sat, 03 Apr 2021 07:12:29: start model_add_line... INFO @ Sat, 03 Apr 2021 07:12:29: start X-correlation... INFO @ Sat, 03 Apr 2021 07:12:29: end of X-cor INFO @ Sat, 03 Apr 2021 07:12:29: #2 finished! INFO @ Sat, 03 Apr 2021 07:12:29: #2 predicted fragment length is 189 bps INFO @ Sat, 03 Apr 2021 07:12:29: #2 alternative fragment length(s) may be 189 bps INFO @ Sat, 03 Apr 2021 07:12:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.05_model.r WARNING @ Sat, 03 Apr 2021 07:12:29: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:12:29: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Sat, 03 Apr 2021 07:12:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:12:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:12:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:12:34: 19000000 INFO @ Sat, 03 Apr 2021 07:12:42: 21000000 INFO @ Sat, 03 Apr 2021 07:12:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:12:46: 20000000 INFO @ Sat, 03 Apr 2021 07:12:54: 22000000 INFO @ Sat, 03 Apr 2021 07:12:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:12:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:12:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.05_summits.bed INFO @ Sat, 03 Apr 2021 07:12:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4000 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:12:59: 21000000 INFO @ Sat, 03 Apr 2021 07:13:06: 23000000 INFO @ Sat, 03 Apr 2021 07:13:11: 22000000 INFO @ Sat, 03 Apr 2021 07:13:13: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 07:13:13: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 07:13:13: #1 total tags in treatment: 8465678 INFO @ Sat, 03 Apr 2021 07:13:13: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:13:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:13:13: #1 tags after filtering in treatment: 6331798 INFO @ Sat, 03 Apr 2021 07:13:13: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:13:13: #1 finished! INFO @ Sat, 03 Apr 2021 07:13:13: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:13:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:13:14: #2 number of paired peaks: 958 WARNING @ Sat, 03 Apr 2021 07:13:14: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sat, 03 Apr 2021 07:13:14: start model_add_line... INFO @ Sat, 03 Apr 2021 07:13:14: start X-correlation... INFO @ Sat, 03 Apr 2021 07:13:14: end of X-cor INFO @ Sat, 03 Apr 2021 07:13:14: #2 finished! INFO @ Sat, 03 Apr 2021 07:13:14: #2 predicted fragment length is 189 bps INFO @ Sat, 03 Apr 2021 07:13:14: #2 alternative fragment length(s) may be 189 bps INFO @ Sat, 03 Apr 2021 07:13:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.10_model.r WARNING @ Sat, 03 Apr 2021 07:13:14: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:13:14: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Sat, 03 Apr 2021 07:13:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:13:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:13:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:13:23: 23000000 INFO @ Sat, 03 Apr 2021 07:13:28: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 07:13:28: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 07:13:28: #1 total tags in treatment: 8465678 INFO @ Sat, 03 Apr 2021 07:13:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:13:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:13:28: #1 tags after filtering in treatment: 6331798 INFO @ Sat, 03 Apr 2021 07:13:28: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:13:28: #1 finished! INFO @ Sat, 03 Apr 2021 07:13:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:13:29: #2 number of paired peaks: 958 WARNING @ Sat, 03 Apr 2021 07:13:29: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sat, 03 Apr 2021 07:13:29: start model_add_line... INFO @ Sat, 03 Apr 2021 07:13:29: start X-correlation... INFO @ Sat, 03 Apr 2021 07:13:29: end of X-cor INFO @ Sat, 03 Apr 2021 07:13:29: #2 finished! INFO @ Sat, 03 Apr 2021 07:13:29: #2 predicted fragment length is 189 bps INFO @ Sat, 03 Apr 2021 07:13:29: #2 alternative fragment length(s) may be 189 bps INFO @ Sat, 03 Apr 2021 07:13:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.20_model.r WARNING @ Sat, 03 Apr 2021 07:13:29: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:13:29: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Sat, 03 Apr 2021 07:13:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:13:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:13:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:13:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:13:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:13:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:13:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.10_summits.bed INFO @ Sat, 03 Apr 2021 07:13:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2285 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:13:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:13:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246269/SRX7246269.20_summits.bed INFO @ Sat, 03 Apr 2021 07:13:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1013 records, 4 fields): 3 millis CompletedMACS2peakCalling