[2023-06-27 06:48:56,816] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:48:56,821] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:48:56,821] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf571c79-0805-411f-a296-c2196c376006/dqc_reference
[2023-06-27 06:48:58,203] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:48:58,204] [INFO] Task started: Prodigal
[2023-06-27 06:48:58,204] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb6bf1d5-164d-4050-95e9-1cf286b2b83a/GCA_027407585.1_ASM2740758v1_genomic.fna.gz | prodigal -d GCA_027407585.1_ASM2740758v1_genomic.fna/cds.fna -a GCA_027407585.1_ASM2740758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:49:09,276] [INFO] Task succeeded: Prodigal
[2023-06-27 06:49:09,276] [INFO] Task started: HMMsearch
[2023-06-27 06:49:09,276] [INFO] Running command: hmmsearch --tblout GCA_027407585.1_ASM2740758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf571c79-0805-411f-a296-c2196c376006/dqc_reference/reference_markers.hmm GCA_027407585.1_ASM2740758v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:49:09,567] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:49:09,568] [INFO] Found 6/6 markers.
[2023-06-27 06:49:09,599] [INFO] Query marker FASTA was written to GCA_027407585.1_ASM2740758v1_genomic.fna/markers.fasta
[2023-06-27 06:49:09,599] [INFO] Task started: Blastn
[2023-06-27 06:49:09,599] [INFO] Running command: blastn -query GCA_027407585.1_ASM2740758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf571c79-0805-411f-a296-c2196c376006/dqc_reference/reference_markers.fasta -out GCA_027407585.1_ASM2740758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:49:10,344] [INFO] Task succeeded: Blastn
[2023-06-27 06:49:10,364] [INFO] Selected 32 target genomes.
[2023-06-27 06:49:10,365] [INFO] Target genome list was writen to GCA_027407585.1_ASM2740758v1_genomic.fna/target_genomes.txt
[2023-06-27 06:49:10,372] [INFO] Task started: fastANI
[2023-06-27 06:49:10,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6bf1d5-164d-4050-95e9-1cf286b2b83a/GCA_027407585.1_ASM2740758v1_genomic.fna.gz --refList GCA_027407585.1_ASM2740758v1_genomic.fna/target_genomes.txt --output GCA_027407585.1_ASM2740758v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:49:35,501] [INFO] Task succeeded: fastANI
[2023-06-27 06:49:35,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf571c79-0805-411f-a296-c2196c376006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:49:35,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf571c79-0805-411f-a296-c2196c376006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:49:35,522] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:49:35,522] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:49:35,523] [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
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.2465	106	1135	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.238	163	1135	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.0696	133	1135	95	below_threshold
Marmoricola solisilvae	strain=KIS18-7	GCA_003725775.1	1542737	1542737	type	True	75.8507	60	1135	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.4518	107	1135	95	below_threshold
Marmoricola ginsengisoli	strain=Gsoil 097	GCA_003725695.1	661483	661483	type	True	75.3967	73	1135	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	75.3818	106	1135	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	75.2841	156	1135	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	75.2361	84	1135	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	75.1911	142	1135	95	below_threshold
Arthrobacter pityocampae	strain=Tp2	GCA_002927275.1	547334	547334	type	True	75.1667	50	1135	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34	GCA_000696595.1	1437453	1437453	type	True	75.1405	133	1135	95	below_threshold
Sinomonas mesophila	strain=MPKL 26	GCA_001999765.1	1531955	1531955	type	True	75.1393	65	1135	95	below_threshold
Streptomyces hirsutus	strain=NRRL B-2713	GCA_001418415.1	35620	35620	type	True	75.1335	106	1135	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	75.1062	76	1135	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	75.0723	126	1135	95	below_threshold
Streptomyces alboflavus	strain=NRRL B-2373	GCA_000716675.1	67267	67267	type	True	75.0699	121	1135	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	75.0673	127	1135	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	75.0602	128	1135	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	75.0097	126	1135	95	below_threshold
Actinocatenispora comari	strain=NUM-2625	GCA_017312725.1	2807577	2807577	type	True	74.9992	154	1135	95	below_threshold
Achromobacter ruhlandii	strain=LMG 1866	GCA_902859695.1	72557	72557	type	True	74.7001	65	1135	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	74.5968	134	1135	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:49:35,525] [INFO] DFAST Taxonomy check result was written to GCA_027407585.1_ASM2740758v1_genomic.fna/tc_result.tsv
[2023-06-27 06:49:35,525] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:49:35,525] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:49:35,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf571c79-0805-411f-a296-c2196c376006/dqc_reference/checkm_data
[2023-06-27 06:49:35,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:49:35,562] [INFO] Task started: CheckM
[2023-06-27 06:49:35,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027407585.1_ASM2740758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027407585.1_ASM2740758v1_genomic.fna/checkm_input GCA_027407585.1_ASM2740758v1_genomic.fna/checkm_result
[2023-06-27 06:50:09,332] [INFO] Task succeeded: CheckM
[2023-06-27 06:50:09,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:50:09,365] [INFO] ===== Completeness check finished =====
[2023-06-27 06:50:09,365] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:50:09,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027407585.1_ASM2740758v1_genomic.fna/markers.fasta)
[2023-06-27 06:50:09,366] [INFO] Task started: Blastn
[2023-06-27 06:50:09,366] [INFO] Running command: blastn -query GCA_027407585.1_ASM2740758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf571c79-0805-411f-a296-c2196c376006/dqc_reference/reference_markers_gtdb.fasta -out GCA_027407585.1_ASM2740758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:50:10,395] [INFO] Task succeeded: Blastn
[2023-06-27 06:50:10,400] [INFO] Selected 27 target genomes.
[2023-06-27 06:50:10,400] [INFO] Target genome list was writen to GCA_027407585.1_ASM2740758v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:50:10,413] [INFO] Task started: fastANI
[2023-06-27 06:50:10,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6bf1d5-164d-4050-95e9-1cf286b2b83a/GCA_027407585.1_ASM2740758v1_genomic.fna.gz --refList GCA_027407585.1_ASM2740758v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027407585.1_ASM2740758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:50:26,209] [INFO] Task succeeded: fastANI
[2023-06-27 06:50:26,231] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:50:26,232] [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_003166025.1	s__Fen-671 sp003166025	77.4689	298	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__Fen-671	95.0	99.76	99.70	0.93	0.92	4	-
GCA_019241495.1	s__JAFAWZ01 sp019241495	76.8351	106	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__JAFAWZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158835.1	s__Fen-671 sp003158835	76.7214	206	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__Fen-671	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888395.1	s__AC-25 sp005888395	76.6139	83	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-25;g__AC-25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781105.1	s__JADDRA01 sp016781105	76.5948	149	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__JADDRA01	95.0	99.25	99.25	0.80	0.80	2	-
GCA_005884125.1	s__AC-35 sp005884125	76.36	176	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-35;g__AC-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888295.1	s__AC-9 sp005888295	76.3043	120	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__QHCF01;g__AC-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009785715.1	s__WQVT01 sp009785715	76.1507	71	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__WQVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.0824	132	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151235.1	s__Palsa-461 sp003151235	76.0439	93	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Palsa-461	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716005.1	s__JADJXE01 sp016716005	76.0377	172	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003156795.1	s__PALSA-688 sp003156795	75.9758	109	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__PALSA-688	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	75.9597	183	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695115.1	s__JACDBD01 sp013695115	75.9107	60	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__JACDBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	75.6368	100	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870245.1	s__CAIUKV01 sp016870245	75.5705	87	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883125.1	s__CAIUMH01 sp017883125	75.5195	54	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__CAIUMH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000931445.1	s__Streptomyces cyaneogriseus	75.4012	124	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.603	N/A	N/A	N/A	N/A	1	-
GCA_016936035.1	s__ZC4RG19 sp016936035	75.359	82	1135	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418415.1	s__Streptomyces hirsutus	75.1404	105	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.60	97.60	0.78	0.78	2	-
GCF_008373755.1	s__Nocardioides sp008373755	75.1062	76	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001865245.1	s__Streptomyces sp001865245	74.9871	116	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.88	98.02	0.87	0.86	3	-
GCF_003696205.1	s__Cellulomonas sp003696205	74.9787	80	1135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	74.7958	63	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 06:50:26,247] [INFO] GTDB search result was written to GCA_027407585.1_ASM2740758v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:50:26,247] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:50:26,252] [INFO] DFAST_QC result json was written to GCA_027407585.1_ASM2740758v1_genomic.fna/dqc_result.json
[2023-06-27 06:50:26,253] [INFO] DFAST_QC completed!
[2023-06-27 06:50:26,253] [INFO] Total running time: 0h1m29s