Job ID = 14159498 SRX = SRX8845625 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7505545 spots for SRR12345970/SRR12345970.sra Written 7505545 spots for SRR12345970/SRR12345970.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159668 ("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: 00:06:47 7505545 reads; of these: 7505545 (100.00%) were paired; of these: 2909944 (38.77%) aligned concordantly 0 times 4079034 (54.35%) aligned concordantly exactly 1 time 516567 (6.88%) aligned concordantly >1 times ---- 2909944 pairs aligned concordantly 0 times; of these: 988367 (33.97%) aligned discordantly 1 time ---- 1921577 pairs aligned 0 times concordantly or discordantly; of these: 3843154 mates make up the pairs; of these: 3357747 (87.37%) aligned 0 times 262147 (6.82%) aligned exactly 1 time 223260 (5.81%) aligned >1 times 77.63% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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 8 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] 876582 / 5522607 = 0.1587 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.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 @ Wed, 08 Dec 2021 22:20:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:20:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:20:58: 1000000 INFO @ Wed, 08 Dec 2021 22:21:03: 2000000 INFO @ Wed, 08 Dec 2021 22:21:08: 3000000 INFO @ Wed, 08 Dec 2021 22:21:13: 4000000 INFO @ Wed, 08 Dec 2021 22:21:18: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:21:23: 6000000 INFO @ Wed, 08 Dec 2021 22:21:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.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 @ Wed, 08 Dec 2021 22:21:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:21:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:21:28: 7000000 INFO @ Wed, 08 Dec 2021 22:21:29: 1000000 INFO @ Wed, 08 Dec 2021 22:21:33: 8000000 INFO @ Wed, 08 Dec 2021 22:21:36: 2000000 INFO @ Wed, 08 Dec 2021 22:21:39: 9000000 INFO @ Wed, 08 Dec 2021 22:21:41: 3000000 INFO @ Wed, 08 Dec 2021 22:21:43: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:21:43: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:21:43: #1 total tags in treatment: 3908188 INFO @ Wed, 08 Dec 2021 22:21:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:21:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:21:43: #1 tags after filtering in treatment: 2868571 INFO @ Wed, 08 Dec 2021 22:21:43: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 08 Dec 2021 22:21:43: #1 finished! INFO @ Wed, 08 Dec 2021 22:21:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:21:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:21:44: #2 number of paired peaks: 3325 INFO @ Wed, 08 Dec 2021 22:21:44: start model_add_line... INFO @ Wed, 08 Dec 2021 22:21:44: start X-correlation... INFO @ Wed, 08 Dec 2021 22:21:44: end of X-cor INFO @ Wed, 08 Dec 2021 22:21:44: #2 finished! INFO @ Wed, 08 Dec 2021 22:21:44: #2 predicted fragment length is 110 bps INFO @ Wed, 08 Dec 2021 22:21:44: #2 alternative fragment length(s) may be 110 bps INFO @ Wed, 08 Dec 2021 22:21:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.05_model.r WARNING @ Wed, 08 Dec 2021 22:21:44: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:21:44: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Wed, 08 Dec 2021 22:21:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:21:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:21:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:21:47: 4000000 INFO @ Wed, 08 Dec 2021 22:21:50: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 22:21:52: 5000000 INFO @ Wed, 08 Dec 2021 22:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.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 @ Wed, 08 Dec 2021 22:21:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:21:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:21:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:21:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:21:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.05_summits.bed INFO @ Wed, 08 Dec 2021 22:21:53: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7455 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:21:58: 6000000 INFO @ Wed, 08 Dec 2021 22:21:59: 1000000 INFO @ Wed, 08 Dec 2021 22:22:04: 7000000 INFO @ Wed, 08 Dec 2021 22:22:05: 2000000 INFO @ Wed, 08 Dec 2021 22:22:09: 8000000 INFO @ Wed, 08 Dec 2021 22:22:11: 3000000 INFO @ Wed, 08 Dec 2021 22:22:15: 9000000 INFO @ Wed, 08 Dec 2021 22:22:17: 4000000 INFO @ Wed, 08 Dec 2021 22:22:21: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:22:21: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:22:21: #1 total tags in treatment: 3908188 INFO @ Wed, 08 Dec 2021 22:22:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:22:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:22:21: #1 tags after filtering in treatment: 2868571 INFO @ Wed, 08 Dec 2021 22:22:21: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 08 Dec 2021 22:22:21: #1 finished! INFO @ Wed, 08 Dec 2021 22:22:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:22:21: #2 number of paired peaks: 3325 INFO @ Wed, 08 Dec 2021 22:22:21: start model_add_line... INFO @ Wed, 08 Dec 2021 22:22:21: start X-correlation... INFO @ Wed, 08 Dec 2021 22:22:21: end of X-cor INFO @ Wed, 08 Dec 2021 22:22:21: #2 finished! INFO @ Wed, 08 Dec 2021 22:22:21: #2 predicted fragment length is 110 bps INFO @ Wed, 08 Dec 2021 22:22:21: #2 alternative fragment length(s) may be 110 bps INFO @ Wed, 08 Dec 2021 22:22:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.10_model.r WARNING @ Wed, 08 Dec 2021 22:22:21: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:22:21: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Wed, 08 Dec 2021 22:22:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:22:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:22:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:22:23: 5000000 INFO @ Wed, 08 Dec 2021 22:22:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:22:29: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:22:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:22:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:22:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.10_summits.bed INFO @ Wed, 08 Dec 2021 22:22:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4834 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:22:35: 7000000 INFO @ Wed, 08 Dec 2021 22:22:41: 8000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:22:47: 9000000 INFO @ Wed, 08 Dec 2021 22:22:52: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:22:52: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:22:52: #1 total tags in treatment: 3908188 INFO @ Wed, 08 Dec 2021 22:22:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:22:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 22:22:52: #1 tags after filtering in treatment: 2868571 INFO @ Wed, 08 Dec 2021 22:22:52: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 08 Dec 2021 22:22:52: #1 finished! INFO @ Wed, 08 Dec 2021 22:22:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:22:52: #2 number of paired peaks: 3325 INFO @ Wed, 08 Dec 2021 22:22:52: start model_add_line... INFO @ Wed, 08 Dec 2021 22:22:52: start X-correlation... INFO @ Wed, 08 Dec 2021 22:22:52: end of X-cor INFO @ Wed, 08 Dec 2021 22:22:52: #2 finished! INFO @ Wed, 08 Dec 2021 22:22:52: #2 predicted fragment length is 110 bps INFO @ Wed, 08 Dec 2021 22:22:52: #2 alternative fragment length(s) may be 110 bps INFO @ Wed, 08 Dec 2021 22:22:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.20_model.r WARNING @ Wed, 08 Dec 2021 22:22:52: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:22:52: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Wed, 08 Dec 2021 22:22:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 22:22:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:22:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:22:59: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:23:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:23:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:23:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845625/SRX8845625.20_summits.bed INFO @ Wed, 08 Dec 2021 22:23:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2580 records, 4 fields): 4 millis CompletedMACS2peakCalling