[2024-01-24 11:36:20,762] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:36:20,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:36:20,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg25f7dab9-3599-4b6b-8aab-dc9614ddf78f/dqc_reference
[2024-01-24 11:36:22,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:36:22,019] [INFO] Task started: Prodigal
[2024-01-24 11:36:22,020] [INFO] Running command: gunzip -c /var/lib/cwl/stg4126ae91-525c-4bba-9728-697684cd4005/GCF_019145495.1_ASM1914549v1_genomic.fna.gz | prodigal -d GCF_019145495.1_ASM1914549v1_genomic.fna/cds.fna -a GCF_019145495.1_ASM1914549v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:44,005] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:44,005] [INFO] Task started: HMMsearch
[2024-01-24 11:36:44,005] [INFO] Running command: hmmsearch --tblout GCF_019145495.1_ASM1914549v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25f7dab9-3599-4b6b-8aab-dc9614ddf78f/dqc_reference/reference_markers.hmm GCF_019145495.1_ASM1914549v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:44,341] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:44,343] [INFO] Found 6/6 markers.
[2024-01-24 11:36:44,437] [INFO] Query marker FASTA was written to GCF_019145495.1_ASM1914549v1_genomic.fna/markers.fasta
[2024-01-24 11:36:44,437] [INFO] Task started: Blastn
[2024-01-24 11:36:44,438] [INFO] Running command: blastn -query GCF_019145495.1_ASM1914549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f7dab9-3599-4b6b-8aab-dc9614ddf78f/dqc_reference/reference_markers.fasta -out GCF_019145495.1_ASM1914549v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:45,292] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:45,295] [INFO] Selected 21 target genomes.
[2024-01-24 11:36:45,295] [INFO] Target genome list was writen to GCF_019145495.1_ASM1914549v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:45,302] [INFO] Task started: fastANI
[2024-01-24 11:36:45,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg4126ae91-525c-4bba-9728-697684cd4005/GCF_019145495.1_ASM1914549v1_genomic.fna.gz --refList GCF_019145495.1_ASM1914549v1_genomic.fna/target_genomes.txt --output GCF_019145495.1_ASM1914549v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:37:13,715] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:13,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25f7dab9-3599-4b6b-8aab-dc9614ddf78f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:37:13,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25f7dab9-3599-4b6b-8aab-dc9614ddf78f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:37:13,735] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:37:13,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:37:13,736] [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 azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	100.0	2237	2238	95	conclusive
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	90.8661	1672	2238	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	90.8651	1673	2238	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	87.8517	1556	2238	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.7303	1603	2238	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	87.7166	1560	2238	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	87.6239	1557	2238	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	87.613	1605	2238	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	87.4585	1526	2238	95	below_threshold
Pseudomonas mohnii	strain=DSM 18327	GCA_900105115.1	395600	395600	type	True	87.3206	1522	2238	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	86.6196	1446	2238	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	86.5713	1418	2238	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.068	1407	2238	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.0594	1459	2238	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.4204	1459	2238	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.2484	1203	2238	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.0395	88	2238	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.0381	68	2238	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.03	90	2238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:37:13,737] [INFO] DFAST Taxonomy check result was written to GCF_019145495.1_ASM1914549v1_genomic.fna/tc_result.tsv
[2024-01-24 11:37:13,738] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:37:13,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:37:13,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25f7dab9-3599-4b6b-8aab-dc9614ddf78f/dqc_reference/checkm_data
[2024-01-24 11:37:13,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:37:13,800] [INFO] Task started: CheckM
[2024-01-24 11:37:13,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019145495.1_ASM1914549v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019145495.1_ASM1914549v1_genomic.fna/checkm_input GCF_019145495.1_ASM1914549v1_genomic.fna/checkm_result
[2024-01-24 11:38:18,927] [INFO] Task succeeded: CheckM
[2024-01-24 11:38:18,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:38:18,954] [INFO] ===== Completeness check finished =====
[2024-01-24 11:38:18,954] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:38:18,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019145495.1_ASM1914549v1_genomic.fna/markers.fasta)
[2024-01-24 11:38:18,955] [INFO] Task started: Blastn
[2024-01-24 11:38:18,955] [INFO] Running command: blastn -query GCF_019145495.1_ASM1914549v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f7dab9-3599-4b6b-8aab-dc9614ddf78f/dqc_reference/reference_markers_gtdb.fasta -out GCF_019145495.1_ASM1914549v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:38:20,362] [INFO] Task succeeded: Blastn
[2024-01-24 11:38:20,367] [INFO] Selected 24 target genomes.
[2024-01-24 11:38:20,368] [INFO] Target genome list was writen to GCF_019145495.1_ASM1914549v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:38:20,429] [INFO] Task started: fastANI
[2024-01-24 11:38:20,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg4126ae91-525c-4bba-9728-697684cd4005/GCF_019145495.1_ASM1914549v1_genomic.fna.gz --refList GCF_019145495.1_ASM1914549v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019145495.1_ASM1914549v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:38:56,355] [INFO] Task succeeded: fastANI
[2024-01-24 11:38:56,379] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:38:56,379] [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_902497845.1	s__Pseudomonas_E fluorescens_BN	98.8061	1945	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.81	0.91	0.91	2	conclusive
GCF_001945365.1	s__Pseudomonas_E reinekei	90.8706	1671	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	95.43	0.93	0.85	5	-
GCF_001427125.1	s__Pseudomonas_E sp001427125	89.7632	1698	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.98	98.83	0.91	0.89	5	-
GCF_000802965.1	s__Pseudomonas_E fluorescens_A	88.5009	1669	2238	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_001429045.1	s__Pseudomonas_E sp001429045	88.0994	1546	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_902498135.1	s__Pseudomonas_E fluorescens_BH	88.0916	1532	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.39	98.07	0.87	0.86	3	-
GCF_000967965.1	s__Pseudomonas_E fluorescens_O	88.0176	1562	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.01	99.01	0.96	0.96	2	-
GCF_000282455.1	s__Pseudomonas_E sp000282455	87.9732	1482	2238	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_002303925.1	s__Pseudomonas_E sp002303925	87.9658	1522	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	99.04	0.91	0.91	2	-
GCF_900187615.1	s__Pseudomonas_E sp900187615	87.9512	1485	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.27	99.27	0.93	0.93	2	-
GCF_002236115.1	s__Pseudomonas_E jessenii	87.8651	1554	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.89	0.89	0.84	18	-
GCF_000282475.1	s__Pseudomonas_E sp000282475	87.8524	1597	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.83	0.83	2	-
GCF_002906155.1	s__Pseudomonas_E laurylsulfativorans	87.7177	1560	2238	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_002934665.1	s__Pseudomonas_E laurylsulfatiphila	87.6064	1606	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.74	0.86	0.82	13	-
GCF_008801475.1	s__Pseudomonas_E moorei	87.4452	1528	2238	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_001269805.1	s__Pseudomonas_E sp001269805	87.2929	1583	2238	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_000968015.1	s__Pseudomonas_E fluorescens_W	87.0044	1516	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.19	96.19	0.86	0.86	2	-
GCF_001238485.1	s__Pseudomonas_E syringae_E	86.4935	1361	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.97	95.90	0.85	0.84	15	-
GCF_014472415.1	s__Pseudomonas_E sp014472415	85.7859	1366	2238	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_009834515.1	s__Pseudomonas_E sp009834515	85.576	1420	2238	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_003732225.1	s__Pseudomonas_E brassicacearum_E	85.1724	1262	2238	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_900636825.1	s__Pseudomonas_E fluorescens_BG	84.8942	1352	2238	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_018614775.1	s__Pseudomonas_E fluorescens_BY	84.1887	1101	2238	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_004682045.1	s__Pseudomonas_E nabeulensis	83.1813	1168	2238	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.61	95.59	0.85	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:38:56,381] [INFO] GTDB search result was written to GCF_019145495.1_ASM1914549v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:38:56,381] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:38:56,386] [INFO] DFAST_QC result json was written to GCF_019145495.1_ASM1914549v1_genomic.fna/dqc_result.json
[2024-01-24 11:38:56,386] [INFO] DFAST_QC completed!
[2024-01-24 11:38:56,386] [INFO] Total running time: 0h2m36s