[2024-01-24 11:36:20,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:36:20,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:36:20,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg81c9344b-d9c2-4cd8-b2b9-d248f2a79a8f/dqc_reference
[2024-01-24 11:36:21,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:36:21,840] [INFO] Task started: Prodigal
[2024-01-24 11:36:21,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg82f85897-2db6-413f-9b32-d5b9de699fb3/GCF_019145205.1_ASM1914520v1_genomic.fna.gz | prodigal -d GCF_019145205.1_ASM1914520v1_genomic.fna/cds.fna -a GCF_019145205.1_ASM1914520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:47,419] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:47,419] [INFO] Task started: HMMsearch
[2024-01-24 11:36:47,420] [INFO] Running command: hmmsearch --tblout GCF_019145205.1_ASM1914520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81c9344b-d9c2-4cd8-b2b9-d248f2a79a8f/dqc_reference/reference_markers.hmm GCF_019145205.1_ASM1914520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:47,745] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:47,746] [INFO] Found 6/6 markers.
[2024-01-24 11:36:47,801] [INFO] Query marker FASTA was written to GCF_019145205.1_ASM1914520v1_genomic.fna/markers.fasta
[2024-01-24 11:36:47,802] [INFO] Task started: Blastn
[2024-01-24 11:36:47,802] [INFO] Running command: blastn -query GCF_019145205.1_ASM1914520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c9344b-d9c2-4cd8-b2b9-d248f2a79a8f/dqc_reference/reference_markers.fasta -out GCF_019145205.1_ASM1914520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:48,689] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:48,693] [INFO] Selected 28 target genomes.
[2024-01-24 11:36:48,694] [INFO] Target genome list was writen to GCF_019145205.1_ASM1914520v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:48,719] [INFO] Task started: fastANI
[2024-01-24 11:36:48,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg82f85897-2db6-413f-9b32-d5b9de699fb3/GCF_019145205.1_ASM1914520v1_genomic.fna.gz --refList GCF_019145205.1_ASM1914520v1_genomic.fna/target_genomes.txt --output GCF_019145205.1_ASM1914520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:37:29,037] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:29,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81c9344b-d9c2-4cd8-b2b9-d248f2a79a8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:37:29,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81c9344b-d9c2-4cd8-b2b9-d248f2a79a8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:37:29,060] [INFO] Found 25 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:37:29,060] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:37:29,061] [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 synxantha	strain=DSM 18928	GCA_001439725.1	47883	47883	type	True	95.4839	1820	2132	95	conclusive
Pseudomonas synxantha	strain=LMG 2190	GCA_900105675.1	47883	47883	type	True	95.4619	1838	2132	95	conclusive
Pseudomonas synxantha	strain=NBRC 3913	GCA_002091795.1	47883	47883	type	True	95.4488	1814	2132	95	conclusive
Pseudomonas synxantha	strain=NCTC10696	GCA_901482615.1	47883	47883	type	True	95.4286	1837	2132	95	conclusive
Pseudomonas libanensis	strain=DSM 17149	GCA_001439685.1	75588	75588	type	True	94.8155	1748	2132	95	below_threshold
Pseudomonas paralactis	strain=DSM 29164	GCA_001439735.1	1615673	1615673	type	True	89.8816	1657	2132	95	below_threshold
Pseudomonas salmasensis	strain=SWRI126	GCA_014268375.2	2745514	2745514	type	True	89.8613	1688	2132	95	below_threshold
Pseudomonas paracarnis	strain=V5/DAB/2/5	GCA_904063055.1	2750625	2750625	type	True	89.7534	1640	2132	95	below_threshold
Pseudomonas lactis	strain=DSM 29167	GCA_001439845.1	1615674	1615674	type	True	89.6954	1696	2132	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	87.9703	1553	2132	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	87.6414	1593	2132	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	87.5908	1573	2132	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	87.5748	1588	2132	95	below_threshold
Pseudomonas canadensis	strain=2-92	GCA_000503215.1	915099	915099	type	True	87.5154	1562	2132	95	below_threshold
Pseudomonas edaphica	strain=RD25	GCA_005863185.1	2006980	2006980	type	True	87.4591	1216	2132	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.373	1572	2132	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_001730615.1	321846	321846	type	True	87.3231	1581	2132	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.5175	1442	2132	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	84.9587	1306	2132	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	83.2841	1247	2132	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	79.6267	864	2132	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	79.5772	881	2132	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	79.553	892	2132	95	below_threshold
Pseudomonas yangmingensis	strain=DSM 24213	GCA_900114825.1	1720063	1720063	type	True	77.3607	228	2132	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	75.7271	62	2132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:37:29,062] [INFO] DFAST Taxonomy check result was written to GCF_019145205.1_ASM1914520v1_genomic.fna/tc_result.tsv
[2024-01-24 11:37:29,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:37:29,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:37:29,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81c9344b-d9c2-4cd8-b2b9-d248f2a79a8f/dqc_reference/checkm_data
[2024-01-24 11:37:29,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:37:29,124] [INFO] Task started: CheckM
[2024-01-24 11:37:29,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019145205.1_ASM1914520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019145205.1_ASM1914520v1_genomic.fna/checkm_input GCF_019145205.1_ASM1914520v1_genomic.fna/checkm_result
[2024-01-24 11:38:40,799] [INFO] Task succeeded: CheckM
[2024-01-24 11:38:40,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:38:40,825] [INFO] ===== Completeness check finished =====
[2024-01-24 11:38:40,825] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:38:40,826] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019145205.1_ASM1914520v1_genomic.fna/markers.fasta)
[2024-01-24 11:38:40,826] [INFO] Task started: Blastn
[2024-01-24 11:38:40,826] [INFO] Running command: blastn -query GCF_019145205.1_ASM1914520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81c9344b-d9c2-4cd8-b2b9-d248f2a79a8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019145205.1_ASM1914520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:38:42,290] [INFO] Task succeeded: Blastn
[2024-01-24 11:38:42,296] [INFO] Selected 27 target genomes.
[2024-01-24 11:38:42,296] [INFO] Target genome list was writen to GCF_019145205.1_ASM1914520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:38:42,316] [INFO] Task started: fastANI
[2024-01-24 11:38:42,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg82f85897-2db6-413f-9b32-d5b9de699fb3/GCF_019145205.1_ASM1914520v1_genomic.fna.gz --refList GCF_019145205.1_ASM1914520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019145205.1_ASM1914520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:39:23,246] [INFO] Task succeeded: fastANI
[2024-01-24 11:39:23,272] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:39:23,272] [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_003851495.1	s__Pseudomonas_E fluorescens_BB	97.6476	1891	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3929	98.85	97.70	0.94	0.89	3	conclusive
GCF_900105675.1	s__Pseudomonas_E synxantha	95.4424	1840	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	98.15	96.46	0.93	0.84	14	-
GCF_001439685.1	s__Pseudomonas_E libanensis	94.8297	1746	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	97.93	95.87	0.95	0.89	3	-
GCF_009659625.1	s__Pseudomonas_E haemolytica	91.0149	1684	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.47	98.83	0.97	0.95	8	-
GCF_000263715.2	s__Pseudomonas_E synxantha_A	90.2654	1730	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.66	97.33	0.90	0.88	8	-
GCF_001439735.1	s__Pseudomonas_E paralactis	89.8813	1657	2132	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_001902145.1	s__Pseudomonas_E fluorescens_BV	89.8471	1649	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.76	95.23	0.87	0.84	22	-
GCF_904063055.1	s__Pseudomonas_E paracarnis	89.755	1640	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	95.59	0.90	0.84	86	-
GCF_001439845.1	s__Pseudomonas_E lactis	89.7028	1695	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	-
GCF_014207255.1	s__Pseudomonas_E sp014207255	88.0392	1546	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.31	98.90	0.95	0.91	5	-
GCF_003097075.1	s__Pseudomonas_E sp003097075	88.0021	1518	2132	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_900105325.1	s__Pseudomonas_E marginalis	87.9217	1589	2132	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_000612585.1	s__Pseudomonas_E sp000612585	87.8385	1513	2132	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_013385965.1	s__Pseudomonas_E edaphica	87.6182	1582	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.93	0.94	0.92	9	-
GCF_900107155.1	s__Pseudomonas_E salomonii	87.567	1590	2132	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_015163715.1	s__Pseudomonas_E cyclaminis	87.4658	1390	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	95.83	0.83	0.80	14	-
GCF_001186335.1	s__Pseudomonas_E trivialis_B	87.4423	1556	2132	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_002563895.1	s__Pseudomonas_E lurida	87.3624	1573	2132	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_019139815.1	s__Pseudomonas_E sp900005815	87.2502	1488	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.55	99.31	0.95	0.92	7	-
GCF_001983175.1	s__Pseudomonas_E cedrina	87.2332	1508	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	97.30	0.97	0.92	4	-
GCF_001439805.1	s__Pseudomonas_E trivialis	86.9226	1415	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.47	95.41	0.96	0.87	4	-
GCF_004519405.1	s__Pseudomonas_E sp004519405	86.7847	1549	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.60	98.40	0.98	0.92	5	-
GCF_009707515.1	s__Pseudomonas_E sp009707515	84.946	1308	2132	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_002018875.1	s__Pseudomonas_E sp002018875	83.502	1316	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.08	96.52	0.93	0.90	4	-
GCF_902497875.1	s__Pseudomonas_E fluorescens_BR	82.7525	1133	2132	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_900114825.1	s__Pseudomonas_D yangmingensis	77.3728	227	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716465.1	s__JADJWH01 sp016716465	75.503	68	2132	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JADJWH01;f__JADJWH01;g__JADJWH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:39:23,274] [INFO] GTDB search result was written to GCF_019145205.1_ASM1914520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:39:23,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:39:23,279] [INFO] DFAST_QC result json was written to GCF_019145205.1_ASM1914520v1_genomic.fna/dqc_result.json
[2024-01-24 11:39:23,279] [INFO] DFAST_QC completed!
[2024-01-24 11:39:23,280] [INFO] Total running time: 0h3m3s