[2023-06-27 05:50:21,322] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:50:21,325] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:50:21,325] [INFO] DQC Reference Directory: /var/lib/cwl/stgd03e9b52-4035-4b85-9fc9-f14841229e06/dqc_reference
[2023-06-27 05:50:22,538] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:50:22,539] [INFO] Task started: Prodigal
[2023-06-27 05:50:22,539] [INFO] Running command: gunzip -c /var/lib/cwl/stg731ea11f-74da-4999-add2-d08739c78a82/GCA_026197035.1_ASM2619703v1_genomic.fna.gz | prodigal -d GCA_026197035.1_ASM2619703v1_genomic.fna/cds.fna -a GCA_026197035.1_ASM2619703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:50:30,150] [INFO] Task succeeded: Prodigal
[2023-06-27 05:50:30,151] [INFO] Task started: HMMsearch
[2023-06-27 05:50:30,151] [INFO] Running command: hmmsearch --tblout GCA_026197035.1_ASM2619703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd03e9b52-4035-4b85-9fc9-f14841229e06/dqc_reference/reference_markers.hmm GCA_026197035.1_ASM2619703v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:50:30,402] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:50:30,404] [INFO] Found 6/6 markers.
[2023-06-27 05:50:30,436] [INFO] Query marker FASTA was written to GCA_026197035.1_ASM2619703v1_genomic.fna/markers.fasta
[2023-06-27 05:50:30,436] [INFO] Task started: Blastn
[2023-06-27 05:50:30,436] [INFO] Running command: blastn -query GCA_026197035.1_ASM2619703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03e9b52-4035-4b85-9fc9-f14841229e06/dqc_reference/reference_markers.fasta -out GCA_026197035.1_ASM2619703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:50:31,309] [INFO] Task succeeded: Blastn
[2023-06-27 05:50:31,314] [INFO] Selected 28 target genomes.
[2023-06-27 05:50:31,315] [INFO] Target genome list was writen to GCA_026197035.1_ASM2619703v1_genomic.fna/target_genomes.txt
[2023-06-27 05:50:31,320] [INFO] Task started: fastANI
[2023-06-27 05:50:31,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg731ea11f-74da-4999-add2-d08739c78a82/GCA_026197035.1_ASM2619703v1_genomic.fna.gz --refList GCA_026197035.1_ASM2619703v1_genomic.fna/target_genomes.txt --output GCA_026197035.1_ASM2619703v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:50:48,394] [INFO] Task succeeded: fastANI
[2023-06-27 05:50:48,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd03e9b52-4035-4b85-9fc9-f14841229e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:50:48,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd03e9b52-4035-4b85-9fc9-f14841229e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:50:48,421] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:50:48,422] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 05:50:48,422] [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
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	78.1437	280	864	95	below_threshold
Thiohalomonas denitrificans	strain=HLD2	GCA_900102855.1	415747	415747	type	True	77.3681	184	864	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.2819	214	864	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.1273	156	864	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.0664	160	864	95	below_threshold
Salinicola endophyticus	strain=CPA92	GCA_003206575.1	1949083	1949083	type	True	77.0107	91	864	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.9496	125	864	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	76.7761	83	864	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	76.7445	100	864	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.6807	121	864	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.5947	143	864	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.544	117	864	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.4901	113	864	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.4893	68	864	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	76.4819	101	864	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	76.439	116	864	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	76.4379	115	864	95	below_threshold
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	76.3864	71	864	95	below_threshold
Halomonas gudaonensis	strain=CGMCC 1.6133	GCA_900100195.1	376427	376427	type	True	76.2913	86	864	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.1602	76	864	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	76.1006	83	864	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	76.0853	66	864	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	76.0558	69	864	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.0144	73	864	95	below_threshold
Halofilum ochraceum	strain=XJ16	GCA_001614315.2	1611323	1611323	type	True	76.0113	56	864	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	75.9359	71	864	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	75.8981	73	864	95	below_threshold
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	75.8205	59	864	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 05:50:48,425] [INFO] DFAST Taxonomy check result was written to GCA_026197035.1_ASM2619703v1_genomic.fna/tc_result.tsv
[2023-06-27 05:50:48,426] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:50:48,426] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:50:48,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd03e9b52-4035-4b85-9fc9-f14841229e06/dqc_reference/checkm_data
[2023-06-27 05:50:48,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:50:48,473] [INFO] Task started: CheckM
[2023-06-27 05:50:48,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026197035.1_ASM2619703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026197035.1_ASM2619703v1_genomic.fna/checkm_input GCA_026197035.1_ASM2619703v1_genomic.fna/checkm_result
[2023-06-27 05:51:16,200] [INFO] Task succeeded: CheckM
[2023-06-27 05:51:16,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:51:16,222] [INFO] ===== Completeness check finished =====
[2023-06-27 05:51:16,222] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:51:16,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026197035.1_ASM2619703v1_genomic.fna/markers.fasta)
[2023-06-27 05:51:16,223] [INFO] Task started: Blastn
[2023-06-27 05:51:16,223] [INFO] Running command: blastn -query GCA_026197035.1_ASM2619703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd03e9b52-4035-4b85-9fc9-f14841229e06/dqc_reference/reference_markers_gtdb.fasta -out GCA_026197035.1_ASM2619703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:51:17,776] [INFO] Task succeeded: Blastn
[2023-06-27 05:51:17,780] [INFO] Selected 19 target genomes.
[2023-06-27 05:51:17,780] [INFO] Target genome list was writen to GCA_026197035.1_ASM2619703v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:51:17,785] [INFO] Task started: fastANI
[2023-06-27 05:51:17,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg731ea11f-74da-4999-add2-d08739c78a82/GCA_026197035.1_ASM2619703v1_genomic.fna.gz --refList GCA_026197035.1_ASM2619703v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026197035.1_ASM2619703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:51:28,045] [INFO] Task succeeded: fastANI
[2023-06-27 05:51:28,065] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 05:51:28,066] [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_007125455.1	s__SLDE01 sp007125455	78.7201	249	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__SLDE01	95.0	99.17	99.17	0.92	0.92	2	-
GCA_002376325.1	s__Sulfurivermis sp002376325	78.1854	191	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	78.1309	281	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859545.1	s__SLDE01 sp014859545	78.0137	226	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__SLDE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	77.9726	286	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003062205.1	s__Sedimenticola_A endophacoides	77.6637	149	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Sedimenticola_A	95.0	99.88	99.76	0.97	0.95	6	-
GCF_900102855.1	s__Thiohalomonas denitrificans	77.3681	184	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Thiohalomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	77.3676	134	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.232	182	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762495.1	s__JABURT01 sp014762495	77.1482	103	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JABURT01;f__JABURT01;g__JABURT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	77.056	135	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCA_003251535.1	s__SZUA-493 sp003251535	76.9746	171	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__SZUA-493	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	76.7445	100	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	76.7175	121	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046015.1	s__SpSt-1174 sp011046015	76.6933	117	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712635.1	s__JADJWH01 sp016712635	76.6765	95	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	76.6389	115	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCA_015487785.1	s__S012-40 sp015487785	76.4632	88	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S140-43;f__S140-43;g__S012-40	95.0	99.75	99.72	0.93	0.92	3	-
GCF_004339665.1	s__Azotobacter chroococcum	76.4214	117	864	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
--------------------------------------------------------------------------------
[2023-06-27 05:51:28,083] [INFO] GTDB search result was written to GCA_026197035.1_ASM2619703v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:51:28,084] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:51:28,110] [INFO] DFAST_QC result json was written to GCA_026197035.1_ASM2619703v1_genomic.fna/dqc_result.json
[2023-06-27 05:51:28,110] [INFO] DFAST_QC completed!
[2023-06-27 05:51:28,111] [INFO] Total running time: 0h1m7s