[2023-06-29 16:30:19,841] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:30:19,843] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:30:19,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg004e7083-8066-468e-8b5c-93eef33fcdf4/dqc_reference
[2023-06-29 16:30:21,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:30:21,167] [INFO] Task started: Prodigal
[2023-06-29 16:30:21,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg04d21f7d-1b2f-4e3a-accd-17fd0b590cf7/GCA_011620185.1_ASM1162018v1_genomic.fna.gz | prodigal -d GCA_011620185.1_ASM1162018v1_genomic.fna/cds.fna -a GCA_011620185.1_ASM1162018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:30:25,036] [INFO] Task succeeded: Prodigal
[2023-06-29 16:30:25,037] [INFO] Task started: HMMsearch
[2023-06-29 16:30:25,037] [INFO] Running command: hmmsearch --tblout GCA_011620185.1_ASM1162018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg004e7083-8066-468e-8b5c-93eef33fcdf4/dqc_reference/reference_markers.hmm GCA_011620185.1_ASM1162018v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:30:25,241] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:30:25,243] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg04d21f7d-1b2f-4e3a-accd-17fd0b590cf7/GCA_011620185.1_ASM1162018v1_genomic.fna.gz]
[2023-06-29 16:30:25,270] [INFO] Query marker FASTA was written to GCA_011620185.1_ASM1162018v1_genomic.fna/markers.fasta
[2023-06-29 16:30:25,271] [INFO] Task started: Blastn
[2023-06-29 16:30:25,271] [INFO] Running command: blastn -query GCA_011620185.1_ASM1162018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg004e7083-8066-468e-8b5c-93eef33fcdf4/dqc_reference/reference_markers.fasta -out GCA_011620185.1_ASM1162018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:30:26,134] [INFO] Task succeeded: Blastn
[2023-06-29 16:30:26,138] [INFO] Selected 21 target genomes.
[2023-06-29 16:30:26,138] [INFO] Target genome list was writen to GCA_011620185.1_ASM1162018v1_genomic.fna/target_genomes.txt
[2023-06-29 16:30:26,173] [INFO] Task started: fastANI
[2023-06-29 16:30:26,173] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d21f7d-1b2f-4e3a-accd-17fd0b590cf7/GCA_011620185.1_ASM1162018v1_genomic.fna.gz --refList GCA_011620185.1_ASM1162018v1_genomic.fna/target_genomes.txt --output GCA_011620185.1_ASM1162018v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:30:39,345] [INFO] Task succeeded: fastANI
[2023-06-29 16:30:39,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg004e7083-8066-468e-8b5c-93eef33fcdf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:30:39,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg004e7083-8066-468e-8b5c-93eef33fcdf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:30:39,363] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:30:39,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:30:39,363] [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
Immundisolibacter cernigliae	strain=TR3.2	GCA_001697225.1	1810504	1810504	type	True	94.9134	307	367	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	76.8032	83	367	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.728	86	367	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.7147	127	367	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	76.7066	98	367	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.68	120	367	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.6132	52	367	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.5848	134	367	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.5554	87	367	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	76.5081	89	367	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.5049	103	367	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.4616	101	367	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	76.4415	51	367	95	below_threshold
Arenimonas donghaensis	strain=HO3-R19	GCA_000743535.1	375061	375061	type	True	76.4083	83	367	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	76.1801	84	367	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.1493	102	367	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	76.0729	107	367	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	76.0474	56	367	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	76.0326	83	367	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.0165	102	367	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	75.8365	61	367	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:30:39,375] [INFO] DFAST Taxonomy check result was written to GCA_011620185.1_ASM1162018v1_genomic.fna/tc_result.tsv
[2023-06-29 16:30:39,376] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:30:39,376] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:30:39,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg004e7083-8066-468e-8b5c-93eef33fcdf4/dqc_reference/checkm_data
[2023-06-29 16:30:39,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:30:39,415] [INFO] Task started: CheckM
[2023-06-29 16:30:39,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011620185.1_ASM1162018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011620185.1_ASM1162018v1_genomic.fna/checkm_input GCA_011620185.1_ASM1162018v1_genomic.fna/checkm_result
[2023-06-29 16:30:58,337] [INFO] Task succeeded: CheckM
[2023-06-29 16:30:58,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.20%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:30:58,358] [INFO] ===== Completeness check finished =====
[2023-06-29 16:30:58,358] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:30:58,359] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011620185.1_ASM1162018v1_genomic.fna/markers.fasta)
[2023-06-29 16:30:58,359] [INFO] Task started: Blastn
[2023-06-29 16:30:58,359] [INFO] Running command: blastn -query GCA_011620185.1_ASM1162018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg004e7083-8066-468e-8b5c-93eef33fcdf4/dqc_reference/reference_markers_gtdb.fasta -out GCA_011620185.1_ASM1162018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:30:59,704] [INFO] Task succeeded: Blastn
[2023-06-29 16:30:59,709] [INFO] Selected 14 target genomes.
[2023-06-29 16:30:59,709] [INFO] Target genome list was writen to GCA_011620185.1_ASM1162018v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:30:59,716] [INFO] Task started: fastANI
[2023-06-29 16:30:59,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d21f7d-1b2f-4e3a-accd-17fd0b590cf7/GCA_011620185.1_ASM1162018v1_genomic.fna.gz --refList GCA_011620185.1_ASM1162018v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011620185.1_ASM1162018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:31:07,375] [INFO] Task succeeded: fastANI
[2023-06-29 16:31:07,393] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:31:07,393] [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_014359565.1	s__Immundisolibacter sp014359565	95.0803	303	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001697225.1	s__Immundisolibacter cernigliae	94.9799	306	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003526065.1	s__Immundisolibacter sp003526065	83.7599	212	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	77.0167	57	367	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	77.0143	86	367	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_018623495.1	s__JAAZVP01 sp018623495	76.8792	66	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	76.7405	117	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	76.5832	134	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429065.1	s__Silanimonas lenta	76.5599	74	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115705.1	s__Frateuria_A terrea	76.509	89	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000743535.1	s__Arenimonas donghaensis	76.3641	85	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013519935.1	s__WFHF3C12 sp013519935	76.2657	55	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__WFHF3C12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046015.1	s__SpSt-1174 sp011046015	76.1491	53	367	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_016208415.1	s__JACQYB01 sp016208415	75.7433	85	367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 16:31:07,395] [INFO] GTDB search result was written to GCA_011620185.1_ASM1162018v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:31:07,396] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:31:07,400] [INFO] DFAST_QC result json was written to GCA_011620185.1_ASM1162018v1_genomic.fna/dqc_result.json
[2023-06-29 16:31:07,401] [INFO] DFAST_QC completed!
[2023-06-29 16:31:07,401] [INFO] Total running time: 0h0m48s