[2023-06-28 00:49:20,436] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:49:20,439] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:49:20,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg206ecbdb-0368-4d99-b68d-fe4a688b5c67/dqc_reference
[2023-06-28 00:49:21,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:49:21,792] [INFO] Task started: Prodigal
[2023-06-28 00:49:21,792] [INFO] Running command: gunzip -c /var/lib/cwl/stgca4bd56e-ae9e-42aa-aae8-ab4a6c049ce9/GCA_026982565.1_ASM2698256v1_genomic.fna.gz | prodigal -d GCA_026982565.1_ASM2698256v1_genomic.fna/cds.fna -a GCA_026982565.1_ASM2698256v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:49:29,307] [INFO] Task succeeded: Prodigal
[2023-06-28 00:49:29,307] [INFO] Task started: HMMsearch
[2023-06-28 00:49:29,308] [INFO] Running command: hmmsearch --tblout GCA_026982565.1_ASM2698256v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg206ecbdb-0368-4d99-b68d-fe4a688b5c67/dqc_reference/reference_markers.hmm GCA_026982565.1_ASM2698256v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:49:29,540] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:49:29,542] [INFO] Found 6/6 markers.
[2023-06-28 00:49:29,571] [INFO] Query marker FASTA was written to GCA_026982565.1_ASM2698256v1_genomic.fna/markers.fasta
[2023-06-28 00:49:29,572] [INFO] Task started: Blastn
[2023-06-28 00:49:29,572] [INFO] Running command: blastn -query GCA_026982565.1_ASM2698256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg206ecbdb-0368-4d99-b68d-fe4a688b5c67/dqc_reference/reference_markers.fasta -out GCA_026982565.1_ASM2698256v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:49:30,424] [INFO] Task succeeded: Blastn
[2023-06-28 00:49:30,428] [INFO] Selected 32 target genomes.
[2023-06-28 00:49:30,429] [INFO] Target genome list was writen to GCA_026982565.1_ASM2698256v1_genomic.fna/target_genomes.txt
[2023-06-28 00:49:30,436] [INFO] Task started: fastANI
[2023-06-28 00:49:30,437] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4bd56e-ae9e-42aa-aae8-ab4a6c049ce9/GCA_026982565.1_ASM2698256v1_genomic.fna.gz --refList GCA_026982565.1_ASM2698256v1_genomic.fna/target_genomes.txt --output GCA_026982565.1_ASM2698256v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:49:50,841] [INFO] Task succeeded: fastANI
[2023-06-28 00:49:50,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg206ecbdb-0368-4d99-b68d-fe4a688b5c67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:49:50,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg206ecbdb-0368-4d99-b68d-fe4a688b5c67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:49:50,866] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:49:50,867] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:49:50,867] [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
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.3774	135	770	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	77.2032	128	770	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	77.0804	122	770	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.9387	88	770	95	below_threshold
Ectothiorhodospira magna	strain=B7-7	GCA_900110965.1	867345	867345	type	True	76.7637	79	770	95	below_threshold
Sulfuricaulis limicola	strain=HA5	GCA_002355735.1	1620215	1620215	type	True	76.7521	66	770	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	76.6622	71	770	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.4217	67	770	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	76.3037	62	770	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.2461	102	770	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	76.1064	69	770	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.0711	50	770	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	76.0465	85	770	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	75.9935	88	770	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.9134	66	770	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	75.8665	59	770	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	75.8213	61	770	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.8126	64	770	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	75.6647	63	770	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.5745	50	770	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:49:50,869] [INFO] DFAST Taxonomy check result was written to GCA_026982565.1_ASM2698256v1_genomic.fna/tc_result.tsv
[2023-06-28 00:49:50,870] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:49:50,871] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:49:50,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg206ecbdb-0368-4d99-b68d-fe4a688b5c67/dqc_reference/checkm_data
[2023-06-28 00:49:50,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:49:50,900] [INFO] Task started: CheckM
[2023-06-28 00:49:50,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026982565.1_ASM2698256v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026982565.1_ASM2698256v1_genomic.fna/checkm_input GCA_026982565.1_ASM2698256v1_genomic.fna/checkm_result
[2023-06-28 00:50:18,129] [INFO] Task succeeded: CheckM
[2023-06-28 00:50:18,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:50:18,151] [INFO] ===== Completeness check finished =====
[2023-06-28 00:50:18,151] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:50:18,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026982565.1_ASM2698256v1_genomic.fna/markers.fasta)
[2023-06-28 00:50:18,152] [INFO] Task started: Blastn
[2023-06-28 00:50:18,152] [INFO] Running command: blastn -query GCA_026982565.1_ASM2698256v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg206ecbdb-0368-4d99-b68d-fe4a688b5c67/dqc_reference/reference_markers_gtdb.fasta -out GCA_026982565.1_ASM2698256v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:50:19,731] [INFO] Task succeeded: Blastn
[2023-06-28 00:50:19,735] [INFO] Selected 25 target genomes.
[2023-06-28 00:50:19,735] [INFO] Target genome list was writen to GCA_026982565.1_ASM2698256v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:50:19,751] [INFO] Task started: fastANI
[2023-06-28 00:50:19,751] [INFO] Running command: fastANI --query /var/lib/cwl/stgca4bd56e-ae9e-42aa-aae8-ab4a6c049ce9/GCA_026982565.1_ASM2698256v1_genomic.fna.gz --refList GCA_026982565.1_ASM2698256v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026982565.1_ASM2698256v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:50:33,434] [INFO] Task succeeded: fastANI
[2023-06-28 00:50:33,457] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:50:33,458] [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_015492435.1	s__SZUA-140 sp015492435	82.6436	444	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-140;f__SZUA-140;g__SZUA-140	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488555.1	s__S012-109 sp015488555	78.391	220	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-140;f__SZUA-140;g__S012-109	95.0	99.64	99.60	0.87	0.87	3	-
GCA_015491615.1	s__S140-43 sp015491615	77.4185	94	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S140-43;f__S140-43;g__S140-43	95.0	99.42	99.32	0.88	0.87	3	-
GCA_016716465.1	s__JADJWH01 sp016716465	77.4091	140	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	77.4044	121	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	77.3564	136	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972985.1	s__Thiolapillus sp003972985	77.3166	86	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus	95.0	99.52	99.52	0.88	0.88	2	-
GCA_011371455.1	s__DRQN01 sp011371455	77.2288	119	770	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	-
GCF_900114895.1	s__Ectothiorhodospira mobilis_A	77.2137	105	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051655.1	s__DRKS01 sp011051655	77.2123	91	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.2035	119	770	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	-
GCF_003337735.1	s__Thioalbus denitrificans	77.2032	128	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584115.1	s__Ectothiorhodospira mobilis	77.0844	110	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Ectothiorhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	77.0804	122	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376325.1	s__Sulfurivermis sp002376325	76.8374	68	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001801995.1	s__YD12-FULL-61-37 sp001801995	76.7818	72	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__YD12-FULL-61-37	95.0	99.93	99.93	0.98	0.98	2	-
GCA_013519935.1	s__WFHF3C12 sp013519935	76.7315	74	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__WFHF3C12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011374975.1	s__Thiogranum sp011374975	76.7113	68	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000934725.1	s__Methyloterricola oryzae	76.6622	71	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methyloterricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762495.1	s__JABURT01 sp014762495	76.3379	58	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JABURT01;f__JABURT01;g__JABURT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378965.1	s__Thioalkalivibrio_A thiocyanodenitrificans	76.2461	102	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412695.1	s__Pseudomonas_F resinovorans_A	76.2282	64	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002113595.1	s__Pseudomonas_E sp002113595	75.8882	56	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	96.42	0.97	0.93	16	-
GCF_000474255.1	s__Pseudomonas_F alcaligenes_A	75.7174	73	770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	98.08	97.69	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-28 00:50:33,460] [INFO] GTDB search result was written to GCA_026982565.1_ASM2698256v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:50:33,460] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:50:33,465] [INFO] DFAST_QC result json was written to GCA_026982565.1_ASM2698256v1_genomic.fna/dqc_result.json
[2023-06-28 00:50:33,465] [INFO] DFAST_QC completed!
[2023-06-28 00:50:33,466] [INFO] Total running time: 0h1m13s