Job ID = 8069460 SRX = SRX8392429 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 'SRR11842082'... 2020-08-08T03:33:11 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:35:44 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:35:44 prefetch.2.10.7: 1) 'SRR11842082' was downloaded successfully 2020-08-08T03:35:44 prefetch.2.10.7: 'SRR11842082' has 0 unresolved dependencies Read 8002944 spots for SRR11842082/SRR11842082.sra Written 8002944 spots for SRR11842082/SRR11842082.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070327 ("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: 00:11:57 8002944 reads; of these: 8002944 (100.00%) were paired; of these: 3238164 (40.46%) aligned concordantly 0 times 4203502 (52.52%) aligned concordantly exactly 1 time 561278 (7.01%) aligned concordantly >1 times ---- 3238164 pairs aligned concordantly 0 times; of these: 1133097 (34.99%) aligned discordantly 1 time ---- 2105067 pairs aligned 0 times concordantly or discordantly; of these: 4210134 mates make up the pairs; of these: 3911291 (92.90%) aligned 0 times 116286 (2.76%) aligned exactly 1 time 182557 (4.34%) aligned >1 times 75.56% overall alignment rate Time searching: 00:11:57 Overall time: 00:11:57 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] 1181175 / 5841012 = 0.2022 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 12:53:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.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 12:53:57: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:53:57: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:54:07: 1000000 INFO @ Sat, 08 Aug 2020 12:54:18: 2000000 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 12:54:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.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 12:54:27: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:54:27: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:54:28: 3000000 INFO @ Sat, 08 Aug 2020 12:54:37: 1000000 INFO @ Sat, 08 Aug 2020 12:54:40: 4000000 INFO @ Sat, 08 Aug 2020 12:54:47: 2000000 INFO @ Sat, 08 Aug 2020 12:54:52: 5000000 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 12:54:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.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 12:54:57: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:54:57: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:54:57: 3000000 INFO @ Sat, 08 Aug 2020 12:55:04: 6000000 INFO @ Sat, 08 Aug 2020 12:55:08: 4000000 INFO @ Sat, 08 Aug 2020 12:55:09: 1000000 INFO @ Sat, 08 Aug 2020 12:55:16: 7000000 INFO @ Sat, 08 Aug 2020 12:55:18: 5000000 INFO @ Sat, 08 Aug 2020 12:55:21: 2000000 INFO @ Sat, 08 Aug 2020 12:55:29: 6000000 INFO @ Sat, 08 Aug 2020 12:55:29: 8000000 INFO @ Sat, 08 Aug 2020 12:55:32: 3000000 INFO @ Sat, 08 Aug 2020 12:55:39: 7000000 INFO @ Sat, 08 Aug 2020 12:55:41: 9000000 INFO @ Sat, 08 Aug 2020 12:55:44: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:55:49: 8000000 INFO @ Sat, 08 Aug 2020 12:55:50: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:55:50: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:55:50: #1 total tags in treatment: 3761327 INFO @ Sat, 08 Aug 2020 12:55:50: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:55:50: #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 12:55:50: #1 tags after filtering in treatment: 3336235 INFO @ Sat, 08 Aug 2020 12:55:50: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:55:50: #1 finished! INFO @ Sat, 08 Aug 2020 12:55:50: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:55:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:55:50: #2 number of paired peaks: 2824 INFO @ Sat, 08 Aug 2020 12:55:50: start model_add_line... INFO @ Sat, 08 Aug 2020 12:55:50: start X-correlation... INFO @ Sat, 08 Aug 2020 12:55:50: end of X-cor INFO @ Sat, 08 Aug 2020 12:55:50: #2 finished! INFO @ Sat, 08 Aug 2020 12:55:50: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 12:55:50: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 08 Aug 2020 12:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.05_model.r WARNING @ Sat, 08 Aug 2020 12:55:50: #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 12:55:50: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Sat, 08 Aug 2020 12:55:50: #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 12:55:50: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:55:56: 5000000 INFO @ Sat, 08 Aug 2020 12:55:59: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:56:00: 9000000 INFO @ Sat, 08 Aug 2020 12:56:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:56:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:56:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.05_summits.bed INFO @ Sat, 08 Aug 2020 12:56:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6239 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:56:07: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:56:07: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:56:07: #1 total tags in treatment: 3761327 INFO @ Sat, 08 Aug 2020 12:56:07: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:56:07: #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 12:56:07: #1 tags after filtering in treatment: 3336235 INFO @ Sat, 08 Aug 2020 12:56:07: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:56:07: #1 finished! INFO @ Sat, 08 Aug 2020 12:56:07: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:56:08: #2 number of paired peaks: 2824 INFO @ Sat, 08 Aug 2020 12:56:08: start model_add_line... INFO @ Sat, 08 Aug 2020 12:56:08: start X-correlation... INFO @ Sat, 08 Aug 2020 12:56:08: end of X-cor INFO @ Sat, 08 Aug 2020 12:56:08: #2 finished! INFO @ Sat, 08 Aug 2020 12:56:08: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 12:56:08: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 08 Aug 2020 12:56:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.10_model.r WARNING @ Sat, 08 Aug 2020 12:56:08: #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 12:56:08: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Sat, 08 Aug 2020 12:56:08: #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 12:56:08: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:56:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:56:08: 6000000 INFO @ Sat, 08 Aug 2020 12:56:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:56:19: 7000000 INFO @ Sat, 08 Aug 2020 12:56:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:56:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:56:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.10_summits.bed INFO @ Sat, 08 Aug 2020 12:56:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3735 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:56:29: 8000000 INFO @ Sat, 08 Aug 2020 12:56:40: 9000000 INFO @ Sat, 08 Aug 2020 12:56:48: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:56:48: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:56:48: #1 total tags in treatment: 3761327 INFO @ Sat, 08 Aug 2020 12:56:48: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:56:48: #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 12:56:48: #1 tags after filtering in treatment: 3336235 INFO @ Sat, 08 Aug 2020 12:56:48: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:56:48: #1 finished! INFO @ Sat, 08 Aug 2020 12:56:48: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:56:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:56:48: #2 number of paired peaks: 2824 INFO @ Sat, 08 Aug 2020 12:56:48: start model_add_line... INFO @ Sat, 08 Aug 2020 12:56:48: start X-correlation... INFO @ Sat, 08 Aug 2020 12:56:48: end of X-cor INFO @ Sat, 08 Aug 2020 12:56:48: #2 finished! INFO @ Sat, 08 Aug 2020 12:56:48: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 12:56:48: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 08 Aug 2020 12:56:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.20_model.r WARNING @ Sat, 08 Aug 2020 12:56:48: #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 12:56:48: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Sat, 08 Aug 2020 12:56:48: #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 12:56:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:56:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:56:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:57:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392429/SRX8392429.20_summits.bed INFO @ Sat, 08 Aug 2020 12:57:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2129 records, 4 fields): 3 millis CompletedMACS2peakCalling