Job ID = 8069432 SRX = SRX8392420 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:45 prefetch.2.10.7: 1) Downloading 'SRR11842073'... 2020-08-08T03:32:45 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:38 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:38 prefetch.2.10.7: 1) 'SRR11842073' was downloaded successfully 2020-08-08T03:35:38 prefetch.2.10.7: 'SRR11842073' has 0 unresolved dependencies Read 8332701 spots for SRR11842073/SRR11842073.sra Written 8332701 spots for SRR11842073/SRR11842073.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070435 ("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: 00:14:19 8332701 reads; of these: 8332701 (100.00%) were paired; of these: 740031 (8.88%) aligned concordantly 0 times 6939247 (83.28%) aligned concordantly exactly 1 time 653423 (7.84%) aligned concordantly >1 times ---- 740031 pairs aligned concordantly 0 times; of these: 308810 (41.73%) aligned discordantly 1 time ---- 431221 pairs aligned 0 times concordantly or discordantly; of these: 862442 mates make up the pairs; of these: 688026 (79.78%) aligned 0 times 107966 (12.52%) aligned exactly 1 time 66450 (7.70%) aligned >1 times 95.87% overall alignment rate Time searching: 00:14:19 Overall time: 00:14:19 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] 1759328 / 7859762 = 0.2238 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 12:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.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 12:57:08: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:08: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:16: 1000000 INFO @ Sat, 08 Aug 2020 12:57:23: 2000000 INFO @ Sat, 08 Aug 2020 12:57:31: 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 12:57:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.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 12:57:38: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:38: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:39: 4000000 INFO @ Sat, 08 Aug 2020 12:57:46: 1000000 INFO @ Sat, 08 Aug 2020 12:57:47: 5000000 INFO @ Sat, 08 Aug 2020 12:57:55: 6000000 INFO @ Sat, 08 Aug 2020 12:57:55: 2000000 INFO @ Sat, 08 Aug 2020 12:58:03: 7000000 INFO @ Sat, 08 Aug 2020 12:58:03: 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 12:58:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.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 12:58:08: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:58:08: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:58:11: 8000000 INFO @ Sat, 08 Aug 2020 12:58:12: 4000000 INFO @ Sat, 08 Aug 2020 12:58:16: 1000000 INFO @ Sat, 08 Aug 2020 12:58:19: 9000000 INFO @ Sat, 08 Aug 2020 12:58:21: 5000000 INFO @ Sat, 08 Aug 2020 12:58:25: 2000000 INFO @ Sat, 08 Aug 2020 12:58:27: 10000000 INFO @ Sat, 08 Aug 2020 12:58:30: 6000000 INFO @ Sat, 08 Aug 2020 12:58:34: 3000000 INFO @ Sat, 08 Aug 2020 12:58:36: 11000000 INFO @ Sat, 08 Aug 2020 12:58:39: 7000000 INFO @ Sat, 08 Aug 2020 12:58:43: 4000000 INFO @ Sat, 08 Aug 2020 12:58:44: 12000000 INFO @ Sat, 08 Aug 2020 12:58:47: 8000000 INFO @ Sat, 08 Aug 2020 12:58:48: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:48: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:48: #1 total tags in treatment: 5868599 INFO @ Sat, 08 Aug 2020 12:58:48: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:48: #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 12:58:48: #1 tags after filtering in treatment: 5303443 INFO @ Sat, 08 Aug 2020 12:58:48: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:58:48: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:48: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:49: #2 number of paired peaks: 3401 INFO @ Sat, 08 Aug 2020 12:58:49: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:49: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:49: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:49: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:49: #2 predicted fragment length is 239 bps INFO @ Sat, 08 Aug 2020 12:58:49: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 08 Aug 2020 12:58:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.05_model.r WARNING @ Sat, 08 Aug 2020 12:58:49: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:49: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 08 Aug 2020 12:58:49: #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 12:58:49: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:52: 5000000 INFO @ Sat, 08 Aug 2020 12:58:56: 9000000 INFO @ Sat, 08 Aug 2020 12:59:00: 6000000 INFO @ Sat, 08 Aug 2020 12:59:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:05: 10000000 INFO @ Sat, 08 Aug 2020 12:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.05_summits.bed INFO @ Sat, 08 Aug 2020 12:59:08: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9882 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:59:08: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:59:13: 11000000 INFO @ Sat, 08 Aug 2020 12:59:17: 8000000 INFO @ Sat, 08 Aug 2020 12:59:21: 12000000 INFO @ Sat, 08 Aug 2020 12:59:25: 9000000 INFO @ Sat, 08 Aug 2020 12:59:25: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:25: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:25: #1 total tags in treatment: 5868599 INFO @ Sat, 08 Aug 2020 12:59:25: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:25: #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 12:59:25: #1 tags after filtering in treatment: 5303443 INFO @ Sat, 08 Aug 2020 12:59:25: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:59:25: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:25: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:26: #2 number of paired peaks: 3401 INFO @ Sat, 08 Aug 2020 12:59:26: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:26: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:26: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:26: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:26: #2 predicted fragment length is 239 bps INFO @ Sat, 08 Aug 2020 12:59:26: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 08 Aug 2020 12:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.10_model.r WARNING @ Sat, 08 Aug 2020 12:59:26: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:26: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 08 Aug 2020 12:59:26: #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 12:59:26: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:59:33: 10000000 INFO @ Sat, 08 Aug 2020 12:59:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:41: 11000000 INFO @ Sat, 08 Aug 2020 12:59:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.10_summits.bed INFO @ Sat, 08 Aug 2020 12:59:47: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7219 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:59:48: 12000000 INFO @ Sat, 08 Aug 2020 12:59:52: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:52: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:52: #1 total tags in treatment: 5868599 INFO @ Sat, 08 Aug 2020 12:59:52: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:52: #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 12:59:52: #1 tags after filtering in treatment: 5303443 INFO @ Sat, 08 Aug 2020 12:59:52: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:59:52: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:52: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:52: #2 number of paired peaks: 3401 INFO @ Sat, 08 Aug 2020 12:59:52: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:52: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:52: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:52: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:52: #2 predicted fragment length is 239 bps INFO @ Sat, 08 Aug 2020 12:59:52: #2 alternative fragment length(s) may be 239 bps INFO @ Sat, 08 Aug 2020 12:59:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.20_model.r WARNING @ Sat, 08 Aug 2020 12:59:52: #2 Since the d (239) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:52: #2 You may need to consider one of the other alternative d(s): 239 WARNING @ Sat, 08 Aug 2020 12:59:52: #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 12:59:52: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:00:05: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:00:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:00:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:00:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392420/SRX8392420.20_summits.bed INFO @ Sat, 08 Aug 2020 13:00:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4253 records, 4 fields): 5 millis CompletedMACS2peakCalling