[2024-01-25 18:12:35,786] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:35,787] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:35,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg36d26fdb-87cc-4956-bc55-d8f82f7c4b75/dqc_reference
[2024-01-25 18:12:36,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:36,902] [INFO] Task started: Prodigal
[2024-01-25 18:12:36,902] [INFO] Running command: gunzip -c /var/lib/cwl/stgc49a2187-0d3c-40ca-931c-b6085305da5a/GCF_028823535.1_ASM2882353v1_genomic.fna.gz | prodigal -d GCF_028823535.1_ASM2882353v1_genomic.fna/cds.fna -a GCF_028823535.1_ASM2882353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:58,834] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:58,834] [INFO] Task started: HMMsearch
[2024-01-25 18:12:58,834] [INFO] Running command: hmmsearch --tblout GCF_028823535.1_ASM2882353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36d26fdb-87cc-4956-bc55-d8f82f7c4b75/dqc_reference/reference_markers.hmm GCF_028823535.1_ASM2882353v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:59,177] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:59,177] [INFO] Found 6/6 markers.
[2024-01-25 18:12:59,236] [INFO] Query marker FASTA was written to GCF_028823535.1_ASM2882353v1_genomic.fna/markers.fasta
[2024-01-25 18:12:59,236] [INFO] Task started: Blastn
[2024-01-25 18:12:59,236] [INFO] Running command: blastn -query GCF_028823535.1_ASM2882353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36d26fdb-87cc-4956-bc55-d8f82f7c4b75/dqc_reference/reference_markers.fasta -out GCF_028823535.1_ASM2882353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:00,204] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:00,207] [INFO] Selected 25 target genomes.
[2024-01-25 18:13:00,207] [INFO] Target genome list was writen to GCF_028823535.1_ASM2882353v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:00,231] [INFO] Task started: fastANI
[2024-01-25 18:13:00,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgc49a2187-0d3c-40ca-931c-b6085305da5a/GCF_028823535.1_ASM2882353v1_genomic.fna.gz --refList GCF_028823535.1_ASM2882353v1_genomic.fna/target_genomes.txt --output GCF_028823535.1_ASM2882353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:38,501] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:38,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36d26fdb-87cc-4956-bc55-d8f82f7c4b75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:38,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36d26fdb-87cc-4956-bc55-d8f82f7c4b75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:38,517] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:13:38,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:13:38,517] [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 umsongensis	strain=DSM 16611	GCA_002236105.1	198618	198618	type	True	90.8279	1774	2503	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	87.8321	1504	2503	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	87.8089	1501	2503	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	87.7874	1598	2503	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.7641	1565	2503	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	87.7194	1550	2503	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	87.5496	1570	2503	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	87.5172	1536	2503	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	87.4496	1544	2503	95	below_threshold
Pseudomonas mohnii	strain=DSM 18327	GCA_900105115.1	395600	395600	type	True	87.368	1570	2503	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	86.5195	1397	2503	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	86.5071	1505	2503	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	86.498	1404	2503	95	below_threshold
Pseudomonas vancouverensis	strain=CCUG 49675	GCA_008801375.1	95300	95300	type	True	86.4274	1485	2503	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	86.4162	1397	2503	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	85.918	1378	2503	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	85.8728	1361	2503	95	below_threshold
Pseudomonas ekonensis	strain=COR58	GCA_019145435.1	2842353	2842353	type	True	85.5883	1348	2503	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	85.1365	1363	2503	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	84.9999	1383	2503	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	84.025	1186	2503	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.3702	1195	2503	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	82.9088	1096	2503	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	82.048	847	2503	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	76.1281	136	2503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:38,519] [INFO] DFAST Taxonomy check result was written to GCF_028823535.1_ASM2882353v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:38,519] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:38,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:38,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36d26fdb-87cc-4956-bc55-d8f82f7c4b75/dqc_reference/checkm_data
[2024-01-25 18:13:38,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:38,589] [INFO] Task started: CheckM
[2024-01-25 18:13:38,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028823535.1_ASM2882353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028823535.1_ASM2882353v1_genomic.fna/checkm_input GCF_028823535.1_ASM2882353v1_genomic.fna/checkm_result
[2024-01-25 18:14:43,439] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:43,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:43,470] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:43,470] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:43,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028823535.1_ASM2882353v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:43,471] [INFO] Task started: Blastn
[2024-01-25 18:14:43,471] [INFO] Running command: blastn -query GCF_028823535.1_ASM2882353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36d26fdb-87cc-4956-bc55-d8f82f7c4b75/dqc_reference/reference_markers_gtdb.fasta -out GCF_028823535.1_ASM2882353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:45,246] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:45,250] [INFO] Selected 30 target genomes.
[2024-01-25 18:14:45,250] [INFO] Target genome list was writen to GCF_028823535.1_ASM2882353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:45,295] [INFO] Task started: fastANI
[2024-01-25 18:14:45,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgc49a2187-0d3c-40ca-931c-b6085305da5a/GCF_028823535.1_ASM2882353v1_genomic.fna.gz --refList GCF_028823535.1_ASM2882353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028823535.1_ASM2882353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:32,295] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:32,313] [INFO] Found 30 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:32,313] [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_001976065.1	s__Pseudomonas_E putida_G	99.211	2054	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.27	99.27	0.91	0.91	2	conclusive
GCF_000282475.1	s__Pseudomonas_E sp000282475	91.2428	1687	2503	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_002236105.1	s__Pseudomonas_E umsongensis	90.8285	1774	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.47	96.72	0.91	0.86	9	-
GCF_000802965.1	s__Pseudomonas_E fluorescens_A	88.3097	1580	2503	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_900187565.1	s__Pseudomonas_E sp900187565	87.9681	1575	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.02	95.89	0.85	0.84	3	-
GCF_001945365.1	s__Pseudomonas_E reinekei	87.8175	1500	2503	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_902497845.1	s__Pseudomonas_E fluorescens_BN	87.7606	1592	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.81	0.91	0.91	2	-
GCF_001429045.1	s__Pseudomonas_E sp001429045	87.7404	1526	2503	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_002236115.1	s__Pseudomonas_E jessenii	87.7268	1548	2503	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_000967965.1	s__Pseudomonas_E fluorescens_O	87.6619	1517	2503	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_002906155.1	s__Pseudomonas_E laurylsulfativorans	87.4184	1548	2503	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_016909445.1	s__Pseudomonas_E stutzeri_A	87.3794	1465	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	96.88	0.84	0.84	2	-
GCF_003050925.1	s__Pseudomonas_E sp003050925	87.3787	1473	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.23	96.92	0.93	0.89	3	-
GCF_900105115.1	s__Pseudomonas_E mohnii	87.378	1569	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	96.18	0.85	0.79	7	-
GCF_003053605.1	s__Pseudomonas_E sp003053605	87.3556	1494	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	96.54	0.88	0.80	4	-
GCF_900187615.1	s__Pseudomonas_E sp900187615	87.3249	1432	2503	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_013359595.1	s__Pseudomonas_E sp013359595	87.2579	1542	2503	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	86.8446	1491	2503	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_902497855.1	s__Pseudomonas_E fluorescens_BI	86.7588	1595	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.52	95.78	0.88	0.82	3	-
GCF_000282375.1	s__Pseudomonas_E sp000282375	86.6034	1362	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.36	96.36	0.86	0.86	2	-
GCF_006438915.1	s__Pseudomonas_E arsenicoxydans_A	86.3766	1510	2503	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_014851765.1	s__Pseudomonas_E sp014851765	86.2032	1450	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.11	98.11	0.90	0.90	2	-
GCF_004006335.1	s__Pseudomonas_E sp002112885	86.0432	1389	2503	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	86.0309	1396	2503	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_010448615.1	s__Pseudomonas_E sp001655595	86.0102	1370	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.61	96.24	0.94	0.90	22	-
GCF_002113125.1	s__Pseudomonas_E sp002113125	85.8998	1376	2503	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_017114825.1	s__Pseudomonas_E gregormendelii	85.614	1409	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.47	97.13	0.88	0.86	8	-
GCF_003852405.1	s__Pseudomonas_E sp003852405	83.7225	1173	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.89	95.89	0.88	0.88	2	-
GCF_009707515.1	s__Pseudomonas_E sp009707515	82.9275	1093	2503	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_900115175.1	s__Marinobacter gudaonensis	76.1383	135	2503	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:32,315] [INFO] GTDB search result was written to GCF_028823535.1_ASM2882353v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:32,316] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:32,320] [INFO] DFAST_QC result json was written to GCF_028823535.1_ASM2882353v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:32,320] [INFO] DFAST_QC completed!
[2024-01-25 18:15:32,320] [INFO] Total running time: 0h2m57s