[2024-01-24 13:57:55,595] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b704e64-7df5-4585-ac62-e11dde786d2f/dqc_reference
[2024-01-24 13:57:56,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:56,954] [INFO] Task started: Prodigal
[2024-01-24 13:57:56,954] [INFO] Running command: gunzip -c /var/lib/cwl/stg40d0c6f2-bc29-4ef3-8d99-4bab6eda5729/GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/cds.fna -a GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:08,580] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:08,580] [INFO] Task started: HMMsearch
[2024-01-24 13:58:08,580] [INFO] Running command: hmmsearch --tblout GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b704e64-7df5-4585-ac62-e11dde786d2f/dqc_reference/reference_markers.hmm GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:08,873] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:08,874] [INFO] Found 6/6 markers.
[2024-01-24 13:58:08,908] [INFO] Query marker FASTA was written to GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:58:08,908] [INFO] Task started: Blastn
[2024-01-24 13:58:08,908] [INFO] Running command: blastn -query GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b704e64-7df5-4585-ac62-e11dde786d2f/dqc_reference/reference_markers.fasta -out GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:10,032] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:10,036] [INFO] Selected 26 target genomes.
[2024-01-24 13:58:10,036] [INFO] Target genome list was writen to GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:10,051] [INFO] Task started: fastANI
[2024-01-24 13:58:10,052] [INFO] Running command: fastANI --query /var/lib/cwl/stg40d0c6f2-bc29-4ef3-8d99-4bab6eda5729/GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna.gz --refList GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:36,462] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:36,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b704e64-7df5-4585-ac62-e11dde786d2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:36,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b704e64-7df5-4585-ac62-e11dde786d2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:36,492] [INFO] Found 26 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:36,493] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:36,493] [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 flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	100.0	1227	1233	95	conclusive
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	99.9893	1214	1233	95	conclusive
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	82.9321	686	1233	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	82.844	702	1233	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	82.6475	787	1233	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.6066	663	1233	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	82.5471	772	1233	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	82.4784	774	1233	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.3739	718	1233	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	82.3126	661	1233	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	82.1532	676	1233	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	82.0903	613	1233	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	82.0812	679	1233	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	81.7223	663	1233	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.5762	713	1233	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	81.5721	722	1233	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.5489	684	1233	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.547	730	1233	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	81.4396	684	1233	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	81.4118	736	1233	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	81.3939	680	1233	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	79.9448	580	1233	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.9549	176	1233	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.9449	178	1233	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	76.4205	232	1233	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	76.3889	221	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,494] [INFO] DFAST Taxonomy check result was written to GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:36,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:36,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:36,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b704e64-7df5-4585-ac62-e11dde786d2f/dqc_reference/checkm_data
[2024-01-24 13:58:36,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:36,538] [INFO] Task started: CheckM
[2024-01-24 13:58:36,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/checkm_input GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:59:14,496] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:14,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:14,514] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:14,515] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:14,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:59:14,515] [INFO] Task started: Blastn
[2024-01-24 13:59:14,516] [INFO] Running command: blastn -query GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b704e64-7df5-4585-ac62-e11dde786d2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:16,497] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:16,502] [INFO] Selected 27 target genomes.
[2024-01-24 13:59:16,502] [INFO] Target genome list was writen to GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:16,525] [INFO] Task started: fastANI
[2024-01-24 13:59:16,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg40d0c6f2-bc29-4ef3-8d99-4bab6eda5729/GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna.gz --refList GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:40,540] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:40,560] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:40,560] [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_000802425.1	s__Pseudomonas_H flexibilis	99.9893	1214	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_H	95.0	99.07	98.74	0.94	0.90	5	conclusive
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	82.9875	720	1233	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_900115715.1	s__Pseudomonas_K sagittaria	82.9501	685	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	82.8293	704	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187975.1	s__Pseudomonas delhiensis	82.6302	787	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	82.6203	748	1233	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_019097855.1	s__Pseudomonas_K sp019097855	82.6034	664	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506505.1	s__Pseudomonas_E sp902506505	82.5006	741	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_900112375.1	s__Pseudomonas citronellolis	82.5005	776	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	82.4786	732	1233	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_000364625.1	s__Pseudomonas_E thermotolerans	82.452	696	1233	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_018398425.1	s__Pseudomonas_E lalucatii	82.3797	718	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_900156545.1	s__Pseudomonas_E alcaligenes_A	82.2151	672	1233	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_002890915.1	s__Pseudomonas_A stutzeri_AF	82.1779	746	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000263395.1	s__Pseudomonas_A stutzeri_C	82.1569	674	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110885.1	s__Azotobacter beijerinckii	82.1413	607	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.34	96.47	0.86	0.85	5	-
GCF_004339665.1	s__Azotobacter chroococcum	82.098	678	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
GCA_002483005.1	s__Pseudomonas_E sp002483005	82.0454	443	1233	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_003595175.1	s__Pseudomonas_E sp003595175	81.5624	682	1233	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_002418465.1	s__Pseudomonas_O sp002418465	81.5412	609	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	81.3929	682	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	81.1689	698	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_001636055.1	s__Pseudomonas_E putida_B	80.4937	568	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.02	97.48	0.91	0.86	13	-
GCF_000800615.1	s__Pseudomonas_E putida_F	80.3544	599	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.83	99.76	0.97	0.96	3	-
GCF_003967275.1	s__Sulfuritortus calidifontis	76.9549	175	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Sulfuritortus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001295775.1	s__AAP99 sp001295775	76.3615	122	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AAP99	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389995.1	s__JAABTG01 sp011389995	76.1562	129	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAABTG01;f__JAABTG01;g__JAABTG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:40,562] [INFO] GTDB search result was written to GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:40,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:40,567] [INFO] DFAST_QC result json was written to GCF_900155995.1_IMG-taxon_2681812811_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:59:40,567] [INFO] DFAST_QC completed!
[2024-01-24 13:59:40,567] [INFO] Total running time: 0h1m45s