Job ID = 8069457 SRX = SRX8392428 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:55 prefetch.2.10.7: 1) Downloading 'SRR11842081'... 2020-08-08T03:32:55 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:33:42 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:33:43 prefetch.2.10.7: 'SRR11842081' is valid 2020-08-08T03:33:43 prefetch.2.10.7: 1) 'SRR11842081' was downloaded successfully 2020-08-08T03:33:43 prefetch.2.10.7: 'SRR11842081' has 0 unresolved dependencies Read 1769208 spots for SRR11842081/SRR11842081.sra Written 1769208 spots for SRR11842081/SRR11842081.sra fastq に変換しました。 bowtie でマッピング中... Your job 8069683 ("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: 00:02:21 1769208 reads; of these: 1769208 (100.00%) were paired; of these: 828622 (46.84%) aligned concordantly 0 times 838648 (47.40%) aligned concordantly exactly 1 time 101938 (5.76%) aligned concordantly >1 times ---- 828622 pairs aligned concordantly 0 times; of these: 233429 (28.17%) aligned discordantly 1 time ---- 595193 pairs aligned 0 times concordantly or discordantly; of these: 1190386 mates make up the pairs; of these: 1127297 (94.70%) aligned 0 times 25850 (2.17%) aligned exactly 1 time 37239 (3.13%) aligned >1 times 68.14% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:22 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_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] 213019 / 1163216 = 0.1831 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 12:37:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.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 12:37:49: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:37:49: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:38:00: 1000000 INFO @ Sat, 08 Aug 2020 12:38:09: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:38:09: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:38:09: #1 total tags in treatment: 760754 INFO @ Sat, 08 Aug 2020 12:38:09: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:38:09: #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 12:38:09: #1 tags after filtering in treatment: 729600 INFO @ Sat, 08 Aug 2020 12:38:09: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 08 Aug 2020 12:38:09: #1 finished! INFO @ Sat, 08 Aug 2020 12:38:09: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:38:09: #2 number of paired peaks: 2857 INFO @ Sat, 08 Aug 2020 12:38:09: start model_add_line... INFO @ Sat, 08 Aug 2020 12:38:09: start X-correlation... INFO @ Sat, 08 Aug 2020 12:38:09: end of X-cor INFO @ Sat, 08 Aug 2020 12:38:09: #2 finished! INFO @ Sat, 08 Aug 2020 12:38:09: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 12:38:09: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 08 Aug 2020 12:38:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.05_model.r WARNING @ Sat, 08 Aug 2020 12:38:09: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:38:09: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Sat, 08 Aug 2020 12:38:09: #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 12:38:09: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:38:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:38:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:38:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:38:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.05_summits.bed INFO @ Sat, 08 Aug 2020 12:38:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1918 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 12:38:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.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 12:38:19: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:38:19: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:38:28: 1000000 INFO @ Sat, 08 Aug 2020 12:38:35: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:38:35: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:38:35: #1 total tags in treatment: 760754 INFO @ Sat, 08 Aug 2020 12:38:35: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:38:35: #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 12:38:35: #1 tags after filtering in treatment: 729600 INFO @ Sat, 08 Aug 2020 12:38:35: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 08 Aug 2020 12:38:35: #1 finished! INFO @ Sat, 08 Aug 2020 12:38:35: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:38:36: #2 number of paired peaks: 2857 INFO @ Sat, 08 Aug 2020 12:38:36: start model_add_line... INFO @ Sat, 08 Aug 2020 12:38:36: start X-correlation... INFO @ Sat, 08 Aug 2020 12:38:36: end of X-cor INFO @ Sat, 08 Aug 2020 12:38:36: #2 finished! INFO @ Sat, 08 Aug 2020 12:38:36: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 12:38:36: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 08 Aug 2020 12:38:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.10_model.r WARNING @ Sat, 08 Aug 2020 12:38:36: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:38:36: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Sat, 08 Aug 2020 12:38:36: #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 12:38:36: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:38:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:38:37: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:38:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:38:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:38:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.10_summits.bed INFO @ Sat, 08 Aug 2020 12:38:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (976 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 12:38:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.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 12:38:50: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:38:50: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:39:00: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:39:10: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:39:10: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:39:10: #1 total tags in treatment: 760754 INFO @ Sat, 08 Aug 2020 12:39:10: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:39:10: #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 12:39:10: #1 tags after filtering in treatment: 729600 INFO @ Sat, 08 Aug 2020 12:39:10: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 08 Aug 2020 12:39:10: #1 finished! INFO @ Sat, 08 Aug 2020 12:39:10: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:39:10: #2 number of paired peaks: 2857 INFO @ Sat, 08 Aug 2020 12:39:10: start model_add_line... INFO @ Sat, 08 Aug 2020 12:39:10: start X-correlation... INFO @ Sat, 08 Aug 2020 12:39:10: end of X-cor INFO @ Sat, 08 Aug 2020 12:39:10: #2 finished! INFO @ Sat, 08 Aug 2020 12:39:10: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 12:39:10: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 08 Aug 2020 12:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.20_model.r WARNING @ Sat, 08 Aug 2020 12:39:10: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:39:10: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Sat, 08 Aug 2020 12:39:10: #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 12:39:10: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:39:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:39:12: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392428/SRX8392428.20_summits.bed INFO @ Sat, 08 Aug 2020 12:39:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 1 millis CompletedMACS2peakCalling