[2023-06-29 14:02:13,674] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:02:13,677] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:02:13,677] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f340238-6f69-4d57-891f-f845d9b70662/dqc_reference
[2023-06-29 14:02:15,049] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:02:15,053] [INFO] Task started: Prodigal
[2023-06-29 14:02:15,054] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaccf2cb-2709-47b1-9d5c-04b81bcf4197/GCA_021737665.1_ASM2173766v1_genomic.fna.gz | prodigal -d GCA_021737665.1_ASM2173766v1_genomic.fna/cds.fna -a GCA_021737665.1_ASM2173766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:02:27,451] [INFO] Task succeeded: Prodigal
[2023-06-29 14:02:27,452] [INFO] Task started: HMMsearch
[2023-06-29 14:02:27,452] [INFO] Running command: hmmsearch --tblout GCA_021737665.1_ASM2173766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f340238-6f69-4d57-891f-f845d9b70662/dqc_reference/reference_markers.hmm GCA_021737665.1_ASM2173766v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:02:27,732] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:02:27,734] [INFO] Found 6/6 markers.
[2023-06-29 14:02:27,770] [INFO] Query marker FASTA was written to GCA_021737665.1_ASM2173766v1_genomic.fna/markers.fasta
[2023-06-29 14:02:27,770] [INFO] Task started: Blastn
[2023-06-29 14:02:27,770] [INFO] Running command: blastn -query GCA_021737665.1_ASM2173766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f340238-6f69-4d57-891f-f845d9b70662/dqc_reference/reference_markers.fasta -out GCA_021737665.1_ASM2173766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:02:28,495] [INFO] Task succeeded: Blastn
[2023-06-29 14:02:28,499] [INFO] Selected 24 target genomes.
[2023-06-29 14:02:28,500] [INFO] Target genome list was writen to GCA_021737665.1_ASM2173766v1_genomic.fna/target_genomes.txt
[2023-06-29 14:02:28,502] [INFO] Task started: fastANI
[2023-06-29 14:02:28,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaccf2cb-2709-47b1-9d5c-04b81bcf4197/GCA_021737665.1_ASM2173766v1_genomic.fna.gz --refList GCA_021737665.1_ASM2173766v1_genomic.fna/target_genomes.txt --output GCA_021737665.1_ASM2173766v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:02:44,110] [INFO] Task succeeded: fastANI
[2023-06-29 14:02:44,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f340238-6f69-4d57-891f-f845d9b70662/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:02:44,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f340238-6f69-4d57-891f-f845d9b70662/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:02:44,134] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:02:44,134] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:02:44,134] [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
Desulfarculus baarsii	strain=DSM 2075	GCA_000143965.1	453230	453230	type	True	78.0541	420	1298	95	below_threshold
Dethiosulfatarculus sandiegensis	strain=SPR	GCA_000931935.2	1429043	1429043	type	True	76.5049	162	1298	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	76.1144	93	1298	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	76.0636	109	1298	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	76.0301	114	1298	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	75.9928	97	1298	95	below_threshold
Desulfacinum hydrothermale	strain=DSM 13146	GCA_900176285.1	109258	109258	type	True	75.9101	88	1298	95	below_threshold
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	75.8813	55	1298	95	below_threshold
Desulfacinum infernum	strain=DSM 9756	GCA_900129305.1	35837	35837	type	True	75.8337	124	1298	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	75.8148	98	1298	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.7913	199	1298	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	75.4496	104	1298	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	75.29	98	1298	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	75.2811	99	1298	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	75.2701	55	1298	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	75.2429	65	1298	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	74.9797	147	1298	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	74.8821	105	1298	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	74.8553	107	1298	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	74.8032	116	1298	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	74.7744	118	1298	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:02:44,136] [INFO] DFAST Taxonomy check result was written to GCA_021737665.1_ASM2173766v1_genomic.fna/tc_result.tsv
[2023-06-29 14:02:44,137] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:02:44,137] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:02:44,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f340238-6f69-4d57-891f-f845d9b70662/dqc_reference/checkm_data
[2023-06-29 14:02:44,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:02:44,178] [INFO] Task started: CheckM
[2023-06-29 14:02:44,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021737665.1_ASM2173766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021737665.1_ASM2173766v1_genomic.fna/checkm_input GCA_021737665.1_ASM2173766v1_genomic.fna/checkm_result
[2023-06-29 14:03:21,789] [INFO] Task succeeded: CheckM
[2023-06-29 14:03:21,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.88%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:03:21,816] [INFO] ===== Completeness check finished =====
[2023-06-29 14:03:21,816] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:03:21,817] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021737665.1_ASM2173766v1_genomic.fna/markers.fasta)
[2023-06-29 14:03:21,817] [INFO] Task started: Blastn
[2023-06-29 14:03:21,817] [INFO] Running command: blastn -query GCA_021737665.1_ASM2173766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f340238-6f69-4d57-891f-f845d9b70662/dqc_reference/reference_markers_gtdb.fasta -out GCA_021737665.1_ASM2173766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:03:23,042] [INFO] Task succeeded: Blastn
[2023-06-29 14:03:23,047] [INFO] Selected 9 target genomes.
[2023-06-29 14:03:23,047] [INFO] Target genome list was writen to GCA_021737665.1_ASM2173766v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:03:23,048] [INFO] Task started: fastANI
[2023-06-29 14:03:23,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaccf2cb-2709-47b1-9d5c-04b81bcf4197/GCA_021737665.1_ASM2173766v1_genomic.fna.gz --refList GCA_021737665.1_ASM2173766v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021737665.1_ASM2173766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:03:30,754] [INFO] Task succeeded: fastANI
[2023-06-29 14:03:30,769] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:03:30,769] [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_018902755.1	s__SURF-10 sp018902755	83.8239	909	1298	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.98	99.96	0.97	0.96	6	-
GCA_018896025.1	s__SURF-10 sp018896025	83.6678	896	1298	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.58	98.82	0.97	0.95	4	-
GCA_018819925.1	s__SURF-10 sp018819925	83.0667	814	1298	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.87	99.83	0.95	0.93	4	-
GCA_003605055.1	s__SURF-10 sp003605055	82.1014	674	1298	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218705.1	s__JACRDC01 sp016218705	79.5272	550	1298	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__JACRDC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001184205.1	s__Desulfocarbo indianensis	79.3319	551	1298	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__Desulfocarbo	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143965.1	s__Desulfarculus baarsii	78.104	413	1298	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__Desulfarculus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823485.1	s__Hydrogenophaga sp013823485	75.0136	76	1298	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	98.29	98.29	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-29 14:03:30,771] [INFO] GTDB search result was written to GCA_021737665.1_ASM2173766v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:03:30,772] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:03:30,776] [INFO] DFAST_QC result json was written to GCA_021737665.1_ASM2173766v1_genomic.fna/dqc_result.json
[2023-06-29 14:03:30,776] [INFO] DFAST_QC completed!
[2023-06-29 14:03:30,776] [INFO] Total running time: 0h1m17s