[2024-01-24 13:21:45,896] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:45,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:45,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg13094a7b-254e-4e1e-92be-8c20cf769435/dqc_reference
[2024-01-24 13:21:47,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:47,240] [INFO] Task started: Prodigal
[2024-01-24 13:21:47,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg583a9972-0cde-4c9a-99c6-d7a59d7b1aa6/GCF_005863185.1_ASM586318v1_genomic.fna.gz | prodigal -d GCF_005863185.1_ASM586318v1_genomic.fna/cds.fna -a GCF_005863185.1_ASM586318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:07,922] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:07,922] [INFO] Task started: HMMsearch
[2024-01-24 13:22:07,923] [INFO] Running command: hmmsearch --tblout GCF_005863185.1_ASM586318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13094a7b-254e-4e1e-92be-8c20cf769435/dqc_reference/reference_markers.hmm GCF_005863185.1_ASM586318v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:08,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:08,352] [INFO] Found 6/6 markers.
[2024-01-24 13:22:08,423] [INFO] Query marker FASTA was written to GCF_005863185.1_ASM586318v1_genomic.fna/markers.fasta
[2024-01-24 13:22:08,423] [INFO] Task started: Blastn
[2024-01-24 13:22:08,424] [INFO] Running command: blastn -query GCF_005863185.1_ASM586318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13094a7b-254e-4e1e-92be-8c20cf769435/dqc_reference/reference_markers.fasta -out GCF_005863185.1_ASM586318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:09,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:09,397] [INFO] Selected 22 target genomes.
[2024-01-24 13:22:09,398] [INFO] Target genome list was writen to GCF_005863185.1_ASM586318v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:09,403] [INFO] Task started: fastANI
[2024-01-24 13:22:09,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg583a9972-0cde-4c9a-99c6-d7a59d7b1aa6/GCF_005863185.1_ASM586318v1_genomic.fna.gz --refList GCF_005863185.1_ASM586318v1_genomic.fna/target_genomes.txt --output GCF_005863185.1_ASM586318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:35,586] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:35,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13094a7b-254e-4e1e-92be-8c20cf769435/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:35,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13094a7b-254e-4e1e-92be-8c20cf769435/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:35,604] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:35,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:35,604] [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 edaphica	strain=RD25	GCA_005863185.1	2006980	2006980	type	True	100.0	1666	1694	95	conclusive
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	94.6009	1424	1694	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	94.5378	1443	1694	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	89.3161	1370	1694	95	below_threshold
Pseudomonas fluorescens	strain=NBRC 14160	GCA_002091595.1	294	294	suspected-type	True	89.2975	1362	1694	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	89.2731	1373	1694	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	88.1117	1257	1694	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	88.017	1285	1694	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.7486	1269	1694	95	below_threshold
Pseudomonas asgharzadehiana	strain=SWRI132	GCA_019139815.1	2842349	2842349	type	True	87.537	1194	1694	95	below_threshold
Pseudomonas yamanorum	strain=LMG 27247	GCA_900105735.1	515393	515393	suspected-type	True	86.8451	1294	1694	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	86.0492	1135	1694	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.9029	1217	1694	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.2633	1041	1694	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	80.4751	717	1694	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	80.4498	716	1694	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	79.7868	543	1694	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	79.752	575	1694	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	75.7808	87	1694	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.7496	86	1694	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.6154	86	1694	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:35,606] [INFO] DFAST Taxonomy check result was written to GCF_005863185.1_ASM586318v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:35,607] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:35,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:35,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13094a7b-254e-4e1e-92be-8c20cf769435/dqc_reference/checkm_data
[2024-01-24 13:22:35,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:35,677] [INFO] Task started: CheckM
[2024-01-24 13:22:35,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005863185.1_ASM586318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005863185.1_ASM586318v1_genomic.fna/checkm_input GCF_005863185.1_ASM586318v1_genomic.fna/checkm_result
[2024-01-24 13:23:35,621] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:35,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:35,647] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:35,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:35,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005863185.1_ASM586318v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:35,648] [INFO] Task started: Blastn
[2024-01-24 13:23:35,649] [INFO] Running command: blastn -query GCF_005863185.1_ASM586318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13094a7b-254e-4e1e-92be-8c20cf769435/dqc_reference/reference_markers_gtdb.fasta -out GCF_005863185.1_ASM586318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:37,009] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:37,013] [INFO] Selected 24 target genomes.
[2024-01-24 13:23:37,014] [INFO] Target genome list was writen to GCF_005863185.1_ASM586318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:37,054] [INFO] Task started: fastANI
[2024-01-24 13:23:37,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg583a9972-0cde-4c9a-99c6-d7a59d7b1aa6/GCF_005863185.1_ASM586318v1_genomic.fna.gz --refList GCF_005863185.1_ASM586318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005863185.1_ASM586318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:12,678] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:12,701] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:12,701] [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_013385965.1	s__Pseudomonas_E edaphica	98.7932	1491	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.93	0.94	0.92	9	conclusive
GCF_900107155.1	s__Pseudomonas_E salomonii	94.5117	1445	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	96.43	0.92	0.87	14	-
GCF_005938045.2	s__Pseudomonas_E sp005938045	94.3947	1435	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.18	95.16	0.86	0.86	3	-
GCF_009707325.1	s__Pseudomonas_E sp002263605	89.609	1255	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.58	0.94	0.94	2	-
GCF_003208475.1	s__Pseudomonas_E sp003208475	89.4673	1332	1694	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_900215245.1	s__Pseudomonas_E fluorescens	89.2474	1376	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.25	0.98	0.92	14	-
GCF_001647715.1	s__Pseudomonas_E antarctica_A	89.2453	1392	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.45	0.91	0.91	2	-
GCF_003852315.1	s__Pseudomonas_E sp003014915	89.0933	1345	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	96.20	0.95	0.91	10	-
GCF_003097075.1	s__Pseudomonas_E sp003097075	88.5725	1249	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCF_002843605.1	s__Pseudomonas_E sp002843605	88.5538	1255	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_900591205.1	s__Pseudomonas_E sp900591205	88.4322	1276	1694	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_900105325.1	s__Pseudomonas_E marginalis	88.2006	1253	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_009866765.1	s__Pseudomonas_E sp009866765	87.8716	1208	1694	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_002563895.1	s__Pseudomonas_E lurida	87.7604	1267	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_009296165.1	s__Pseudomonas_E kitaguniensis	87.457	1127	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.01	96.76	0.90	0.88	5	-
GCF_001439735.1	s__Pseudomonas_E paralactis	87.4122	1247	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.52	0.94	0.92	4	-
GCF_007858275.1	s__Pseudomonas_E proteolytica	86.0355	1136	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.69	98.38	0.90	0.86	19	-
GCF_013403585.1	s__Pseudomonas_E yamanorum_B	85.8623	1213	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.31	98.31	0.89	0.89	2	-
GCF_009707515.1	s__Pseudomonas_E sp009707515	85.2633	1041	1694	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_003732265.1	s__Pseudomonas_E brassicacearum_D	83.5746	947	1694	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_008801475.1	s__Pseudomonas_E moorei	83.0999	924	1694	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_902497875.1	s__Pseudomonas_E fluorescens_BR	83.0916	903	1694	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_003428805.1	s__Pseudomonas_E sp003428805	80.8567	772	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	96.05	0.90	0.83	9	-
GCF_018449655.1	s__Pseudomonas_E sp018449655	80.6875	674	1694	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:12,703] [INFO] GTDB search result was written to GCF_005863185.1_ASM586318v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:12,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:12,708] [INFO] DFAST_QC result json was written to GCF_005863185.1_ASM586318v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:12,708] [INFO] DFAST_QC completed!
[2024-01-24 13:24:12,708] [INFO] Total running time: 0h2m27s