[2024-01-24 12:21:44,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,164] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg9eec8bb0-6abc-4852-8082-f4d81fdab213/dqc_reference
[2024-01-24 12:21:45,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,680] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,680] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf51220d-6932-4ac8-a5a7-9fab1cd58504/GCF_003596405.1_ASM359640v1_genomic.fna.gz | prodigal -d GCF_003596405.1_ASM359640v1_genomic.fna/cds.fna -a GCF_003596405.1_ASM359640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:03,915] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:03,915] [INFO] Task started: HMMsearch
[2024-01-24 12:22:03,915] [INFO] Running command: hmmsearch --tblout GCF_003596405.1_ASM359640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9eec8bb0-6abc-4852-8082-f4d81fdab213/dqc_reference/reference_markers.hmm GCF_003596405.1_ASM359640v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:04,309] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:04,310] [INFO] Found 6/6 markers.
[2024-01-24 12:22:04,369] [INFO] Query marker FASTA was written to GCF_003596405.1_ASM359640v1_genomic.fna/markers.fasta
[2024-01-24 12:22:04,369] [INFO] Task started: Blastn
[2024-01-24 12:22:04,370] [INFO] Running command: blastn -query GCF_003596405.1_ASM359640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eec8bb0-6abc-4852-8082-f4d81fdab213/dqc_reference/reference_markers.fasta -out GCF_003596405.1_ASM359640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:05,337] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:05,342] [INFO] Selected 25 target genomes.
[2024-01-24 12:22:05,342] [INFO] Target genome list was writen to GCF_003596405.1_ASM359640v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:05,351] [INFO] Task started: fastANI
[2024-01-24 12:22:05,351] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf51220d-6932-4ac8-a5a7-9fab1cd58504/GCF_003596405.1_ASM359640v1_genomic.fna.gz --refList GCF_003596405.1_ASM359640v1_genomic.fna/target_genomes.txt --output GCF_003596405.1_ASM359640v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:37,511] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:37,512] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9eec8bb0-6abc-4852-8082-f4d81fdab213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:37,512] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9eec8bb0-6abc-4852-8082-f4d81fdab213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:37,532] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:37,532] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:37,533] [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
Pseudomonas cavernicola	strain=K1S02-6	GCA_003596405.1	2320866	2320866	type	True	100.0	1862	1872	95	conclusive
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.7418	1105	1872	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	81.9703	1050	1872	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.6219	916	1872	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	81.5595	968	1872	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.5486	912	1872	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	81.5149	904	1872	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	81.3154	862	1872	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	80.904	853	1872	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	80.7245	855	1872	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	80.5927	810	1872	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	80.5804	823	1872	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	80.509	810	1872	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	80.4459	903	1872	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	80.3149	724	1872	95	below_threshold
Pseudomonas alkylphenolica	strain=KL28	GCA_000746525.1	237609	237609	type	True	80.2755	738	1872	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	80.2637	642	1872	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	80.1365	827	1872	95	below_threshold
Pseudomonas yamanorum	strain=LMG 27247	GCA_900105735.1	515393	515393	suspected-type	True	80.0596	732	1872	95	below_threshold
Pseudomonas tehranensis	strain=SWRI196	GCA_014268615.1	2745502	2745502	type	True	79.877	624	1872	95	below_threshold
Pseudomonas cichorii	strain=DSM 50259	GCA_018343775.1	36746	36746	suspected-type	True	79.7766	572	1872	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	79.6284	620	1872	95	below_threshold
Pseudomonas syringae group genomosp. 3	strain=ICMP3956	GCA_001400635.1	251701	251701	pathovar	True	79.5475	585	1872	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	79.5329	564	1872	95	below_threshold
Pseudomonas cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	79.5037	566	1872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:37,534] [INFO] DFAST Taxonomy check result was written to GCF_003596405.1_ASM359640v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:37,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:37,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:37,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9eec8bb0-6abc-4852-8082-f4d81fdab213/dqc_reference/checkm_data
[2024-01-24 12:22:37,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:37,599] [INFO] Task started: CheckM
[2024-01-24 12:22:37,599] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003596405.1_ASM359640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003596405.1_ASM359640v1_genomic.fna/checkm_input GCF_003596405.1_ASM359640v1_genomic.fna/checkm_result
[2024-01-24 12:23:29,034] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:29,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:29,060] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:29,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:29,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003596405.1_ASM359640v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:29,061] [INFO] Task started: Blastn
[2024-01-24 12:23:29,061] [INFO] Running command: blastn -query GCF_003596405.1_ASM359640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9eec8bb0-6abc-4852-8082-f4d81fdab213/dqc_reference/reference_markers_gtdb.fasta -out GCF_003596405.1_ASM359640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:30,548] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:30,553] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:30,554] [INFO] Target genome list was writen to GCF_003596405.1_ASM359640v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:30,572] [INFO] Task started: fastANI
[2024-01-24 12:23:30,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf51220d-6932-4ac8-a5a7-9fab1cd58504/GCF_003596405.1_ASM359640v1_genomic.fna.gz --refList GCF_003596405.1_ASM359640v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003596405.1_ASM359640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:56,661] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:56,677] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:56,677] [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
GCF_003596405.1	s__Pseudomonas_E sp003596405	100.0	1862	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005502935.1	s__Pseudomonas_E sp005502935	91.0081	1121	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.83	0.83	2	-
GCF_003050835.1	s__Pseudomonas_E sp003050835	81.9836	944	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	81.7664	892	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	81.6036	933	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCF_013184545.1	s__Pseudomonas_E sp013184545	81.5584	967	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901015.1	s__Pseudomonas_E sp016901015	81.5263	916	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993865.1	s__Pseudomonas_E sp007993865	81.4491	948	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174475.1	s__Pseudomonas_E sp014174475	81.2875	865	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900573885.1	s__Pseudomonas_E sp900573885	81.0686	851	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900156545.1	s__Pseudomonas_E alcaligenes_A	80.9018	774	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCF_003208235.1	s__Pseudomonas_E sp003208235	80.7681	834	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407925.2	s__Pseudomonas_E fluorescens_AP	80.7072	809	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	98.42	0.98	0.91	6	-
GCF_000397205.1	s__Pseudomonas_E protegens	80.5443	810	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	97.08	0.96	0.89	76	-
GCF_900105185.1	s__Pseudomonas_E saponiphila	80.4353	823	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.25	98.25	0.89	0.89	5	-
GCF_014863585.1	s__Pseudomonas_E gozinkensis	80.3363	774	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003732485.1	s__Pseudomonas_E protegens_B	80.3345	778	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019145475.1	s__Pseudomonas_E sp019145475	80.2866	772	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001186335.1	s__Pseudomonas_E trivialis_B	79.9359	703	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.34	95.31	0.86	0.86	8	-
GCF_000281895.1	s__Pseudomonas_E fluorescens_S	79.8957	709	1872	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.50	99.50	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:56,679] [INFO] GTDB search result was written to GCF_003596405.1_ASM359640v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:56,680] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:56,684] [INFO] DFAST_QC result json was written to GCF_003596405.1_ASM359640v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:56,684] [INFO] DFAST_QC completed!
[2024-01-24 12:23:56,684] [INFO] Total running time: 0h2m13s