Job ID = 8069463 SRX = SRX8392430 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 'SRR11842083'... 2020-08-08T03:33:11 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:59 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:59 prefetch.2.10.7: 1) 'SRR11842083' was downloaded successfully 2020-08-08T03:34:59 prefetch.2.10.7: 'SRR11842083' has 0 unresolved dependencies Read 7482444 spots for SRR11842083/SRR11842083.sra Written 7482444 spots for SRR11842083/SRR11842083.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070246 ("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: 00:11:18 7482444 reads; of these: 7482444 (100.00%) were paired; of these: 2692281 (35.98%) aligned concordantly 0 times 4250176 (56.80%) aligned concordantly exactly 1 time 539987 (7.22%) aligned concordantly >1 times ---- 2692281 pairs aligned concordantly 0 times; of these: 786519 (29.21%) aligned discordantly 1 time ---- 1905762 pairs aligned 0 times concordantly or discordantly; of these: 3811524 mates make up the pairs; of these: 3580655 (93.94%) aligned 0 times 100764 (2.64%) aligned exactly 1 time 130105 (3.41%) aligned >1 times 76.07% overall alignment rate Time searching: 00:11:18 Overall time: 00:11:18 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] 1211684 / 5534272 = 0.2189 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 12:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.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 12:51:59: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:51:59: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:07: 1000000 INFO @ Sat, 08 Aug 2020 12:52:15: 2000000 INFO @ Sat, 08 Aug 2020 12:52:23: 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 12:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.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 12:52:29: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:29: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:32: 4000000 INFO @ Sat, 08 Aug 2020 12:52:39: 1000000 INFO @ Sat, 08 Aug 2020 12:52:41: 5000000 INFO @ Sat, 08 Aug 2020 12:52:49: 2000000 INFO @ Sat, 08 Aug 2020 12:52:51: 6000000 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 12:52:58: 3000000 INFO @ Sat, 08 Aug 2020 12:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.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 12:52:59: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:59: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:53:00: 7000000 INFO @ Sat, 08 Aug 2020 12:53:08: 4000000 INFO @ Sat, 08 Aug 2020 12:53:09: 1000000 INFO @ Sat, 08 Aug 2020 12:53:10: 8000000 INFO @ Sat, 08 Aug 2020 12:53:18: 5000000 INFO @ Sat, 08 Aug 2020 12:53:19: 2000000 INFO @ Sat, 08 Aug 2020 12:53:20: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:53:20: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:53:20: #1 total tags in treatment: 3709050 INFO @ Sat, 08 Aug 2020 12:53:20: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:20: #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 12:53:20: #1 tags after filtering in treatment: 3321206 INFO @ Sat, 08 Aug 2020 12:53:20: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:53:20: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:20: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:20: #2 number of paired peaks: 2703 INFO @ Sat, 08 Aug 2020 12:53:20: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:20: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:20: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:20: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:20: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:53:20: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.05_model.r WARNING @ Sat, 08 Aug 2020 12:53:20: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:53:20: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 12:53:20: #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 12:53:20: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:53:28: 6000000 INFO @ Sat, 08 Aug 2020 12:53:28: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:53:29: 3000000 INFO @ Sat, 08 Aug 2020 12:53:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:53:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:53:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.05_summits.bed INFO @ Sat, 08 Aug 2020 12:53:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5967 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:53:38: 7000000 INFO @ Sat, 08 Aug 2020 12:53:39: 4000000 INFO @ Sat, 08 Aug 2020 12:53:48: 8000000 INFO @ Sat, 08 Aug 2020 12:53:49: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:53:57: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:53:57: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:53:57: #1 total tags in treatment: 3709050 INFO @ Sat, 08 Aug 2020 12:53:57: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:53:57: #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 12:53:57: #1 tags after filtering in treatment: 3321206 INFO @ Sat, 08 Aug 2020 12:53:57: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:53:57: #1 finished! INFO @ Sat, 08 Aug 2020 12:53:57: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:53:57: #2 number of paired peaks: 2703 INFO @ Sat, 08 Aug 2020 12:53:57: start model_add_line... INFO @ Sat, 08 Aug 2020 12:53:57: start X-correlation... INFO @ Sat, 08 Aug 2020 12:53:57: end of X-cor INFO @ Sat, 08 Aug 2020 12:53:57: #2 finished! INFO @ Sat, 08 Aug 2020 12:53:57: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:53:57: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.10_model.r WARNING @ Sat, 08 Aug 2020 12:53:57: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:53:57: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 12:53:57: #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 12:53:57: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:53:59: 6000000 INFO @ Sat, 08 Aug 2020 12:54:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:54:08: 7000000 INFO @ Sat, 08 Aug 2020 12:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.10_summits.bed INFO @ Sat, 08 Aug 2020 12:54:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3656 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:54:16: 8000000 INFO @ Sat, 08 Aug 2020 12:54:25: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:54:25: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:54:25: #1 total tags in treatment: 3709050 INFO @ Sat, 08 Aug 2020 12:54:25: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:54:25: #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 12:54:25: #1 tags after filtering in treatment: 3321206 INFO @ Sat, 08 Aug 2020 12:54:25: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:54:25: #1 finished! INFO @ Sat, 08 Aug 2020 12:54:25: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:54:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:54:25: #2 number of paired peaks: 2703 INFO @ Sat, 08 Aug 2020 12:54:25: start model_add_line... INFO @ Sat, 08 Aug 2020 12:54:25: start X-correlation... INFO @ Sat, 08 Aug 2020 12:54:25: end of X-cor INFO @ Sat, 08 Aug 2020 12:54:25: #2 finished! INFO @ Sat, 08 Aug 2020 12:54:25: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:54:25: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:54:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.20_model.r WARNING @ Sat, 08 Aug 2020 12:54:25: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:54:25: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 12:54:25: #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 12:54:25: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:54:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:54:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:54:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:54:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:54:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392430/SRX8392430.20_summits.bed INFO @ Sat, 08 Aug 2020 12:54:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1966 records, 4 fields): 4 millis CompletedMACS2peakCalling