Job ID = 8069389 SRX = SRX7217787 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:31:59 prefetch.2.10.7: 1) Downloading 'SRR10533864'... 2020-08-08T03:31:59 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:33:51 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:33:51 prefetch.2.10.7: 1) 'SRR10533864' was downloaded successfully 2020-08-08T03:33:51 prefetch.2.10.7: 'SRR10533864' has 0 unresolved dependencies Read 6709555 spots for SRR10533864/SRR10533864.sra Written 6709555 spots for SRR10533864/SRR10533864.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070226 ("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: 00:12:04 6709555 reads; of these: 6709555 (100.00%) were paired; of these: 1675199 (24.97%) aligned concordantly 0 times 4256614 (63.44%) aligned concordantly exactly 1 time 777742 (11.59%) aligned concordantly >1 times ---- 1675199 pairs aligned concordantly 0 times; of these: 525986 (31.40%) aligned discordantly 1 time ---- 1149213 pairs aligned 0 times concordantly or discordantly; of these: 2298426 mates make up the pairs; of these: 2038750 (88.70%) aligned 0 times 139922 (6.09%) aligned exactly 1 time 119754 (5.21%) aligned >1 times 84.81% overall alignment rate Time searching: 00:12:04 Overall time: 00:12:04 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 12 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] 738651 / 5521446 = 0.1338 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.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, 08 Aug 2020 12:51:43: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:51:43: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:51:52: 1000000 INFO @ Sat, 08 Aug 2020 12:52:00: 2000000 INFO @ Sat, 08 Aug 2020 12:52:08: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.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, 08 Aug 2020 12:52:13: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:13: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:16: 4000000 INFO @ Sat, 08 Aug 2020 12:52:22: 1000000 INFO @ Sat, 08 Aug 2020 12:52:26: 5000000 INFO @ Sat, 08 Aug 2020 12:52:31: 2000000 INFO @ Sat, 08 Aug 2020 12:52:35: 6000000 INFO @ Sat, 08 Aug 2020 12:52:40: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.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, 08 Aug 2020 12:52:43: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:43: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:44: 7000000 INFO @ Sat, 08 Aug 2020 12:52:50: 4000000 INFO @ Sat, 08 Aug 2020 12:52:54: 1000000 INFO @ Sat, 08 Aug 2020 12:52:55: 8000000 INFO @ Sat, 08 Aug 2020 12:53:01: 5000000 INFO @ Sat, 08 Aug 2020 12:53:05: 2000000 INFO @ Sat, 08 Aug 2020 12:53:05: 9000000 INFO @ Sat, 08 Aug 2020 12:53:11: 6000000 INFO @ Sat, 08 Aug 2020 12:53:14: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:53:14: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:53:14: #1 total tags in treatment: 4347984 INFO @ Sat, 08 Aug 2020 12:53:14: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:53:14: #1 tags after filtering in treatment: 4028665 INFO @ Sat, 08 Aug 2020 12:53:14: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:53:14: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:14: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:15: #2 number of paired peaks: 446 WARNING @ Sat, 08 Aug 2020 12:53:15: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sat, 08 Aug 2020 12:53:15: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:15: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:15: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:15: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:15: #2 predicted fragment length is 211 bps INFO @ Sat, 08 Aug 2020 12:53:15: #2 alternative fragment length(s) may be 211 bps INFO @ Sat, 08 Aug 2020 12:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.05_model.r WARNING @ Sat, 08 Aug 2020 12:53:15: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:53:15: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Sat, 08 Aug 2020 12:53:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:53:15: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:53:16: 3000000 INFO @ Sat, 08 Aug 2020 12:53:21: 7000000 INFO @ Sat, 08 Aug 2020 12:53:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:53:28: 4000000 INFO @ Sat, 08 Aug 2020 12:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.05_summits.bed INFO @ Sat, 08 Aug 2020 12:53:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (365 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:53:31: 8000000 INFO @ Sat, 08 Aug 2020 12:53:39: 5000000 INFO @ Sat, 08 Aug 2020 12:53:41: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:53:50: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:53:50: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:53:50: #1 total tags in treatment: 4347984 INFO @ Sat, 08 Aug 2020 12:53:50: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:53:50: #1 tags after filtering in treatment: 4028665 INFO @ Sat, 08 Aug 2020 12:53:50: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:53:50: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:50: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:50: #2 number of paired peaks: 446 WARNING @ Sat, 08 Aug 2020 12:53:50: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sat, 08 Aug 2020 12:53:50: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:50: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:50: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:50: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:50: #2 predicted fragment length is 211 bps INFO @ Sat, 08 Aug 2020 12:53:50: #2 alternative fragment length(s) may be 211 bps INFO @ Sat, 08 Aug 2020 12:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.10_model.r WARNING @ Sat, 08 Aug 2020 12:53:50: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:53:50: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Sat, 08 Aug 2020 12:53:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:53:50: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:53:51: 6000000 INFO @ Sat, 08 Aug 2020 12:53:59: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:54:02: 7000000 INFO @ Sat, 08 Aug 2020 12:54:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.10_summits.bed INFO @ Sat, 08 Aug 2020 12:54:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:54:12: 8000000 INFO @ Sat, 08 Aug 2020 12:54:23: 9000000 INFO @ Sat, 08 Aug 2020 12:54:32: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:54:32: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:54:32: #1 total tags in treatment: 4347984 INFO @ Sat, 08 Aug 2020 12:54:32: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:54:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:54:32: #1 tags after filtering in treatment: 4028665 INFO @ Sat, 08 Aug 2020 12:54:32: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:54:32: #1 finished! INFO @ Sat, 08 Aug 2020 12:54:32: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:54:33: #2 number of paired peaks: 446 WARNING @ Sat, 08 Aug 2020 12:54:33: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Sat, 08 Aug 2020 12:54:33: start model_add_line... INFO @ Sat, 08 Aug 2020 12:54:33: start X-correlation... INFO @ Sat, 08 Aug 2020 12:54:33: end of X-cor INFO @ Sat, 08 Aug 2020 12:54:33: #2 finished! INFO @ Sat, 08 Aug 2020 12:54:33: #2 predicted fragment length is 211 bps INFO @ Sat, 08 Aug 2020 12:54:33: #2 alternative fragment length(s) may be 211 bps INFO @ Sat, 08 Aug 2020 12:54:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.20_model.r WARNING @ Sat, 08 Aug 2020 12:54:33: #2 Since the d (211) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:54:33: #2 You may need to consider one of the other alternative d(s): 211 WARNING @ Sat, 08 Aug 2020 12:54:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:54:33: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:54:42: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217787/SRX7217787.20_summits.bed INFO @ Sat, 08 Aug 2020 12:54:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling