[2024-01-24 15:26:38,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:38,950] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:38,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg7da26036-fd16-4afe-8676-b16aaa6a1065/dqc_reference
[2024-01-24 15:26:40,414] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,415] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,415] [INFO] Running command: gunzip -c /var/lib/cwl/stg1490c19e-ac37-4ff6-bc01-214ba39db7c3/GCF_019145475.1_ASM1914547v1_genomic.fna.gz | prodigal -d GCF_019145475.1_ASM1914547v1_genomic.fna/cds.fna -a GCF_019145475.1_ASM1914547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:03,041] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:03,041] [INFO] Task started: HMMsearch
[2024-01-24 15:27:03,041] [INFO] Running command: hmmsearch --tblout GCF_019145475.1_ASM1914547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7da26036-fd16-4afe-8676-b16aaa6a1065/dqc_reference/reference_markers.hmm GCF_019145475.1_ASM1914547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:03,416] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:03,418] [INFO] Found 6/6 markers.
[2024-01-24 15:27:03,471] [INFO] Query marker FASTA was written to GCF_019145475.1_ASM1914547v1_genomic.fna/markers.fasta
[2024-01-24 15:27:03,472] [INFO] Task started: Blastn
[2024-01-24 15:27:03,472] [INFO] Running command: blastn -query GCF_019145475.1_ASM1914547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7da26036-fd16-4afe-8676-b16aaa6a1065/dqc_reference/reference_markers.fasta -out GCF_019145475.1_ASM1914547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:04,467] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:04,471] [INFO] Selected 21 target genomes.
[2024-01-24 15:27:04,472] [INFO] Target genome list was writen to GCF_019145475.1_ASM1914547v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:04,482] [INFO] Task started: fastANI
[2024-01-24 15:27:04,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg1490c19e-ac37-4ff6-bc01-214ba39db7c3/GCF_019145475.1_ASM1914547v1_genomic.fna.gz --refList GCF_019145475.1_ASM1914547v1_genomic.fna/target_genomes.txt --output GCF_019145475.1_ASM1914547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:36,851] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:36,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7da26036-fd16-4afe-8676-b16aaa6a1065/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:36,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7da26036-fd16-4afe-8676-b16aaa6a1065/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:36,868] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:36,868] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:36,868] [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 allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	89.3277	1752	2122	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	89.2923	1713	2122	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	89.2661	1641	2122	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	89.2266	1711	2122	95	below_threshold
Pseudomonas bananamidigenes	strain=BW11P2	GCA_001679645.1	2843610	2843610	type	True	88.5451	1607	2122	95	below_threshold
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	88.4666	1662	2122	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	88.4596	1652	2122	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	88.4278	1657	2122	95	below_threshold
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	88.3692	1672	2122	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	87.8427	1720	2122	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	87.5523	1706	2122	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	87.2123	1526	2122	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	87.0069	1581	2122	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	86.1613	1443	2122	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	86.0818	1465	2122	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	85.9097	1421	2122	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	85.892	1411	2122	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	84.1948	1313	2122	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	83.4046	1243	2122	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	82.8533	1137	2122	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.3547	889	2122	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:36,878] [INFO] DFAST Taxonomy check result was written to GCF_019145475.1_ASM1914547v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:36,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:36,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:36,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7da26036-fd16-4afe-8676-b16aaa6a1065/dqc_reference/checkm_data
[2024-01-24 15:27:36,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:36,942] [INFO] Task started: CheckM
[2024-01-24 15:27:36,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019145475.1_ASM1914547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019145475.1_ASM1914547v1_genomic.fna/checkm_input GCF_019145475.1_ASM1914547v1_genomic.fna/checkm_result
[2024-01-24 15:28:45,123] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:45,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:45,159] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:45,160] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:45,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019145475.1_ASM1914547v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:45,162] [INFO] Task started: Blastn
[2024-01-24 15:28:45,162] [INFO] Running command: blastn -query GCF_019145475.1_ASM1914547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7da26036-fd16-4afe-8676-b16aaa6a1065/dqc_reference/reference_markers_gtdb.fasta -out GCF_019145475.1_ASM1914547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:46,962] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:46,965] [INFO] Selected 20 target genomes.
[2024-01-24 15:28:46,965] [INFO] Target genome list was writen to GCF_019145475.1_ASM1914547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:46,981] [INFO] Task started: fastANI
[2024-01-24 15:28:46,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg1490c19e-ac37-4ff6-bc01-214ba39db7c3/GCF_019145475.1_ASM1914547v1_genomic.fna.gz --refList GCF_019145475.1_ASM1914547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019145475.1_ASM1914547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:18,435] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:18,462] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:18,462] [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_019145475.1	s__Pseudomonas_E sp019145475	100.0	2117	2122	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_004006335.1	s__Pseudomonas_E sp002112885	89.5646	1743	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_014863585.1	s__Pseudomonas_E gozinkensis	89.3909	1735	2122	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_003352875.1	s__Pseudomonas_E fluorescens_BF	89.3735	1734	2122	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_001594225.2	s__Pseudomonas_E glycinae	89.3265	1709	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.56	95.98	0.93	0.88	9	-
GCF_014863605.1	s__Pseudomonas_E allokribbensis	89.3024	1755	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.76	0.93	0.92	10	-
GCF_003352185.1	s__Pseudomonas_E kribbensis	89.2729	1716	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.22	95.68	0.92	0.89	10	-
GCF_002113125.1	s__Pseudomonas_E sp002113125	89.2312	1720	2122	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_002113045.1	s__Pseudomonas_E sp002113045	89.0892	1665	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.93	0.93	2	-
GCF_012974785.1	s__Pseudomonas_E fluorescens_BT	88.9921	1749	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.87	0.96	0.96	2	-
GCF_000282275.2	s__Pseudomonas_E sp000282275	88.4511	1651	2122	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_003061005.1	s__Pseudomonas_E sp003061005	88.4497	1544	2122	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_003999415.1	s__Pseudomonas_E koreensis_E	88.3857	1632	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
GCF_004683905.1	s__Pseudomonas_E putida_A	88.3577	1666	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.80	95.08	0.93	0.90	22	-
GCF_000292795.1	s__Pseudomonas_E fluorescens_H	88.3272	1672	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.99	97.99	0.94	0.93	3	-
GCF_002287825.1	s__Pseudomonas_E koreensis_B	88.2873	1663	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.58	96.55	0.92	0.86	13	-
GCF_013359595.1	s__Pseudomonas_E sp013359595	86.52	1423	2122	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_001655615.1	s__Pseudomonas_E sp001655615	86.0823	1535	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	96.99	0.93	0.87	27	-
GCF_001297125.1	s__Pseudomonas_E sp001297125	86.0126	1494	2122	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_013403585.1	s__Pseudomonas_E yamanorum_B	83.2854	1291	2122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.31	98.31	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:18,464] [INFO] GTDB search result was written to GCF_019145475.1_ASM1914547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:18,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:18,469] [INFO] DFAST_QC result json was written to GCF_019145475.1_ASM1914547v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:18,469] [INFO] DFAST_QC completed!
[2024-01-24 15:29:18,469] [INFO] Total running time: 0h2m40s