Job ID = 8069466 SRX = SRX8392431 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:33:11 prefetch.2.10.7: 1) Downloading 'SRR11842084'... 2020-08-08T03:33:11 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:55 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:55 prefetch.2.10.7: 1) 'SRR11842084' was downloaded successfully 2020-08-08T03:35:55 prefetch.2.10.7: 'SRR11842084' has 0 unresolved dependencies Read 10228115 spots for SRR11842084/SRR11842084.sra Written 10228115 spots for SRR11842084/SRR11842084.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070425 ("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: 00:13:31 10228115 reads; of these: 10228115 (100.00%) were paired; of these: 4696718 (45.92%) aligned concordantly 0 times 4962170 (48.52%) aligned concordantly exactly 1 time 569227 (5.57%) aligned concordantly >1 times ---- 4696718 pairs aligned concordantly 0 times; of these: 1570678 (33.44%) aligned discordantly 1 time ---- 3126040 pairs aligned 0 times concordantly or discordantly; of these: 6252080 mates make up the pairs; of these: 5849840 (93.57%) aligned 0 times 163216 (2.61%) aligned exactly 1 time 239024 (3.82%) aligned >1 times 71.40% overall alignment rate Time searching: 00:13:32 Overall time: 00:13:32 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] 1625378 / 7033933 = 0.2311 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 12:56:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.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 12:56:47: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:47: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:56: 1000000 INFO @ Sat, 08 Aug 2020 12:57:04: 2000000 INFO @ Sat, 08 Aug 2020 12:57:13: 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 12:57:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.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 12:57:17: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:17: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:23: 4000000 INFO @ Sat, 08 Aug 2020 12:57:29: 1000000 INFO @ Sat, 08 Aug 2020 12:57:35: 5000000 INFO @ Sat, 08 Aug 2020 12:57:42: 2000000 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 12:57:46: 6000000 INFO @ Sat, 08 Aug 2020 12:57:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.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 12:57:47: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:47: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:56: 3000000 INFO @ Sat, 08 Aug 2020 12:57:58: 7000000 INFO @ Sat, 08 Aug 2020 12:57:58: 1000000 INFO @ Sat, 08 Aug 2020 12:58:09: 4000000 INFO @ Sat, 08 Aug 2020 12:58:10: 8000000 INFO @ Sat, 08 Aug 2020 12:58:10: 2000000 INFO @ Sat, 08 Aug 2020 12:58:21: 9000000 INFO @ Sat, 08 Aug 2020 12:58:22: 5000000 INFO @ Sat, 08 Aug 2020 12:58:23: 3000000 INFO @ Sat, 08 Aug 2020 12:58:32: 10000000 INFO @ Sat, 08 Aug 2020 12:58:34: 4000000 INFO @ Sat, 08 Aug 2020 12:58:35: 6000000 INFO @ Sat, 08 Aug 2020 12:58:44: 11000000 INFO @ Sat, 08 Aug 2020 12:58:45: 5000000 BedGraph に変換しました。 BigWig に変換中... 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: 4193531 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: 7000000 INFO @ Sat, 08 Aug 2020 12:58:48: #1 tags after filtering in treatment: 3612892 INFO @ Sat, 08 Aug 2020 12:58:48: #1 Redundant rate of treatment: 0.14 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 12:58:48: #2 number of paired peaks: 3737 INFO @ Sat, 08 Aug 2020 12:58:48: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:48: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:48: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:48: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:48: #2 predicted fragment length is 195 bps INFO @ Sat, 08 Aug 2020 12:58:48: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 08 Aug 2020 12:58:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.05_model.r WARNING @ Sat, 08 Aug 2020 12:58:48: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:48: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 08 Aug 2020 12:58:48: #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 12:58:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:56: 6000000 INFO @ Sat, 08 Aug 2020 12:58:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:00: 8000000 INFO @ Sat, 08 Aug 2020 12:59:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.05_summits.bed INFO @ Sat, 08 Aug 2020 12:59:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7892 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:59:07: 7000000 INFO @ Sat, 08 Aug 2020 12:59:13: 9000000 INFO @ Sat, 08 Aug 2020 12:59:18: 8000000 INFO @ Sat, 08 Aug 2020 12:59:26: 10000000 INFO @ Sat, 08 Aug 2020 12:59:29: 9000000 INFO @ Sat, 08 Aug 2020 12:59:38: 11000000 INFO @ Sat, 08 Aug 2020 12:59:39: 10000000 INFO @ Sat, 08 Aug 2020 12:59:42: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:42: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:42: #1 total tags in treatment: 4193531 INFO @ Sat, 08 Aug 2020 12:59:42: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:42: #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 12:59:42: #1 tags after filtering in treatment: 3612892 INFO @ Sat, 08 Aug 2020 12:59:42: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 08 Aug 2020 12:59:42: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:42: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:43: #2 number of paired peaks: 3737 INFO @ Sat, 08 Aug 2020 12:59:43: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:43: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:43: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:43: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:43: #2 predicted fragment length is 195 bps INFO @ Sat, 08 Aug 2020 12:59:43: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 08 Aug 2020 12:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.10_model.r WARNING @ Sat, 08 Aug 2020 12:59:43: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:43: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 08 Aug 2020 12:59:43: #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 12:59:43: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:49: 11000000 INFO @ Sat, 08 Aug 2020 12:59:53: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:53: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:53: #1 total tags in treatment: 4193531 INFO @ Sat, 08 Aug 2020 12:59:53: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:53: #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 12:59:53: #1 tags after filtering in treatment: 3612892 INFO @ Sat, 08 Aug 2020 12:59:53: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 08 Aug 2020 12:59:53: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:53: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:53: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:53: #2 number of paired peaks: 3737 INFO @ Sat, 08 Aug 2020 12:59:53: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:53: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:53: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:53: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:53: #2 predicted fragment length is 195 bps INFO @ Sat, 08 Aug 2020 12:59:53: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 08 Aug 2020 12:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.20_model.r WARNING @ Sat, 08 Aug 2020 12:59:53: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:53: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 08 Aug 2020 12:59:53: #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 12:59:53: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.10_summits.bed INFO @ Sat, 08 Aug 2020 12:59:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5120 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:00:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:00:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:00:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392431/SRX8392431.20_summits.bed INFO @ Sat, 08 Aug 2020 13:00:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2911 records, 4 fields): 4 millis CompletedMACS2peakCalling