[2024-01-24 14:03:08,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a9300be-0c8b-4934-b127-94e205dff3bb/dqc_reference
[2024-01-24 14:03:09,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,736] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,736] [INFO] Running command: gunzip -c /var/lib/cwl/stg4cbbbe81-4a70-4acc-b6b2-1261f37614cd/GCF_014857905.1_ASM1485790v1_genomic.fna.gz | prodigal -d GCF_014857905.1_ASM1485790v1_genomic.fna/cds.fna -a GCF_014857905.1_ASM1485790v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:21,068] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:21,069] [INFO] Task started: HMMsearch
[2024-01-24 14:03:21,069] [INFO] Running command: hmmsearch --tblout GCF_014857905.1_ASM1485790v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a9300be-0c8b-4934-b127-94e205dff3bb/dqc_reference/reference_markers.hmm GCF_014857905.1_ASM1485790v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:21,391] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:21,392] [INFO] Found 6/6 markers.
[2024-01-24 14:03:21,447] [INFO] Query marker FASTA was written to GCF_014857905.1_ASM1485790v1_genomic.fna/markers.fasta
[2024-01-24 14:03:21,447] [INFO] Task started: Blastn
[2024-01-24 14:03:21,447] [INFO] Running command: blastn -query GCF_014857905.1_ASM1485790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a9300be-0c8b-4934-b127-94e205dff3bb/dqc_reference/reference_markers.fasta -out GCF_014857905.1_ASM1485790v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:22,716] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:22,719] [INFO] Selected 26 target genomes.
[2024-01-24 14:03:22,719] [INFO] Target genome list was writen to GCF_014857905.1_ASM1485790v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:22,737] [INFO] Task started: fastANI
[2024-01-24 14:03:22,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cbbbe81-4a70-4acc-b6b2-1261f37614cd/GCF_014857905.1_ASM1485790v1_genomic.fna.gz --refList GCF_014857905.1_ASM1485790v1_genomic.fna/target_genomes.txt --output GCF_014857905.1_ASM1485790v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:42,630] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:42,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a9300be-0c8b-4934-b127-94e205dff3bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:42,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a9300be-0c8b-4934-b127-94e205dff3bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:42,656] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:03:42,657] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:03:42,657] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Mobilicoccus pelagius	strain=NBRC 104925	GCA_000247995.2	746032	746032	type	True	79.3546	580	1396	95	below_threshold
Mobilicoccus massiliensis	strain=SIT2	GCA_000826525.2	1522310	1522310	type	True	79.2954	577	1396	95	below_threshold
Kineosphaera limosa	strain=DSM 14548	GCA_013409325.1	111564	111564	type	True	79.1385	640	1396	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.8679	484	1396	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.6814	459	1396	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	78.666	486	1396	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.6617	550	1396	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	78.619	463	1396	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	78.6007	418	1396	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	78.5611	492	1396	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	78.3	390	1396	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.2527	522	1396	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	78.2407	448	1396	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	78.2101	421	1396	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	78.1764	463	1396	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	78.1298	467	1396	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	78.0884	478	1396	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	78.0509	402	1396	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	77.9951	553	1396	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.6828	357	1396	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	77.594	415	1396	95	below_threshold
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	76.9414	410	1396	95	below_threshold
Cellulomonas timonensis	strain=SN7	GCA_900046455.1	1689271	1689271	type	True	76.7885	339	1396	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	76.7357	400	1396	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	76.7127	402	1396	95	below_threshold
Kineococcus xinjiangensis	strain=DSM 22857	GCA_002934625.1	512762	512762	type	True	76.6424	406	1396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:42,659] [INFO] DFAST Taxonomy check result was written to GCF_014857905.1_ASM1485790v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:42,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:42,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:42,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a9300be-0c8b-4934-b127-94e205dff3bb/dqc_reference/checkm_data
[2024-01-24 14:03:42,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:42,706] [INFO] Task started: CheckM
[2024-01-24 14:03:42,707] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014857905.1_ASM1485790v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014857905.1_ASM1485790v1_genomic.fna/checkm_input GCF_014857905.1_ASM1485790v1_genomic.fna/checkm_result
[2024-01-24 14:04:37,537] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:37,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:37,562] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:37,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:37,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014857905.1_ASM1485790v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:37,564] [INFO] Task started: Blastn
[2024-01-24 14:04:37,564] [INFO] Running command: blastn -query GCF_014857905.1_ASM1485790v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a9300be-0c8b-4934-b127-94e205dff3bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014857905.1_ASM1485790v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:39,579] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:39,583] [INFO] Selected 21 target genomes.
[2024-01-24 14:04:39,583] [INFO] Target genome list was writen to GCF_014857905.1_ASM1485790v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:39,615] [INFO] Task started: fastANI
[2024-01-24 14:04:39,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cbbbe81-4a70-4acc-b6b2-1261f37614cd/GCF_014857905.1_ASM1485790v1_genomic.fna.gz --refList GCF_014857905.1_ASM1485790v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014857905.1_ASM1485790v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:57,154] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:57,174] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:57,175] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_014857905.1	s__JACYXE01 sp014857905	100.0	1394	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JACYXE01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001515525.1	s__Piscicoccus intestinalis	79.8043	646	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Piscicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000247995.1	s__Mobilicoccus pelagius	79.3145	585	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Mobilicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826525.2	s__Mobilicoccus massiliensis	79.2837	577	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Mobilicoccus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000298215.1	s__Kineosphaera limosa	79.0859	636	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kineosphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000768675.1	s__Knoellia flava	78.6248	485	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.5882	560	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCA_014763705.1	s__Phycicoccus sp014763705	78.4504	409	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955875.1	s__Terrabacter sp000955875	78.4156	519	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991735.1	s__Terrabacter aerolatus	78.3793	508	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887965.1	s__Phycicoccus sp016887965	78.3773	589	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189535.1	s__Arsenicicoccus sp001189535	78.3143	475	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721155.3	s__Marihabitans melonis	78.3102	526	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCF_000768685.1	s__Knoellia subterranea	78.2814	393	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699675.1	s__Austwickia sp016699675	78.2615	489	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Austwickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139485.1	s__Phycicoccus sp018139485	78.1774	510	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591405.1	s__Janibacter terrae	78.0901	474	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	98.98	98.88	0.95	0.93	4	-
GCF_004025965.2	s__Phycicoccus flavus	77.9826	555	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956915.1	s__Monashia flava	77.8705	504	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906315.1	s__Kineococcus vitellinus	76.9916	403	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934625.1	s__Kineococcus xinjiangensis	76.6589	403	1396	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineococcaceae;g__Kineococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:57,176] [INFO] GTDB search result was written to GCF_014857905.1_ASM1485790v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:57,177] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:57,182] [INFO] DFAST_QC result json was written to GCF_014857905.1_ASM1485790v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:57,183] [INFO] DFAST_QC completed!
[2024-01-24 14:04:57,183] [INFO] Total running time: 0h1m49s