[2024-01-24 15:02:23,267] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,269] [INFO] DQC Reference Directory: /var/lib/cwl/stg27c93815-937b-44ed-b0b9-0d48406bc900/dqc_reference
[2024-01-24 15:02:24,535] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:24,536] [INFO] Task started: Prodigal
[2024-01-24 15:02:24,537] [INFO] Running command: gunzip -c /var/lib/cwl/stg45cc70a6-bbf8-4228-b867-3535f549c151/GCF_003940825.1_ASM394082v1_genomic.fna.gz | prodigal -d GCF_003940825.1_ASM394082v1_genomic.fna/cds.fna -a GCF_003940825.1_ASM394082v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:47,205] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:47,206] [INFO] Task started: HMMsearch
[2024-01-24 15:02:47,206] [INFO] Running command: hmmsearch --tblout GCF_003940825.1_ASM394082v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27c93815-937b-44ed-b0b9-0d48406bc900/dqc_reference/reference_markers.hmm GCF_003940825.1_ASM394082v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:47,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:47,634] [INFO] Found 6/6 markers.
[2024-01-24 15:02:47,711] [INFO] Query marker FASTA was written to GCF_003940825.1_ASM394082v1_genomic.fna/markers.fasta
[2024-01-24 15:02:47,711] [INFO] Task started: Blastn
[2024-01-24 15:02:47,712] [INFO] Running command: blastn -query GCF_003940825.1_ASM394082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27c93815-937b-44ed-b0b9-0d48406bc900/dqc_reference/reference_markers.fasta -out GCF_003940825.1_ASM394082v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:48,812] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:48,815] [INFO] Selected 20 target genomes.
[2024-01-24 15:02:48,816] [INFO] Target genome list was writen to GCF_003940825.1_ASM394082v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:48,828] [INFO] Task started: fastANI
[2024-01-24 15:02:48,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg45cc70a6-bbf8-4228-b867-3535f549c151/GCF_003940825.1_ASM394082v1_genomic.fna.gz --refList GCF_003940825.1_ASM394082v1_genomic.fna/target_genomes.txt --output GCF_003940825.1_ASM394082v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:21,591] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:21,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27c93815-937b-44ed-b0b9-0d48406bc900/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:21,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27c93815-937b-44ed-b0b9-0d48406bc900/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:21,608] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:21,609] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:03:21,609] [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 oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	100.0	2016	2016	95	inconclusive
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	96.2454	1663	2016	95	inconclusive
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	88.989	1451	2016	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	88.9005	1533	2016	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	88.8984	1438	2016	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	88.865	1462	2016	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	88.7666	1459	2016	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	88.6718	1405	2016	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.7968	1299	2016	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	87.7065	1381	2016	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.6371	1373	2016	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	86.5817	1285	2016	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.5591	1338	2016	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	85.7397	1303	2016	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	85.7273	1318	2016	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	83.9965	1253	2016	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	77.1465	189	2016	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	76.727	91	2016	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	75.9922	119	2016	95	below_threshold
Rahnella laticis	strain=SAP-17	GCA_015644585.1	2787622	2787622	type	True	75.6611	61	2016	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:21,611] [INFO] DFAST Taxonomy check result was written to GCF_003940825.1_ASM394082v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:21,611] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:21,611] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:21,612] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27c93815-937b-44ed-b0b9-0d48406bc900/dqc_reference/checkm_data
[2024-01-24 15:03:21,613] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:21,679] [INFO] Task started: CheckM
[2024-01-24 15:03:21,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003940825.1_ASM394082v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003940825.1_ASM394082v1_genomic.fna/checkm_input GCF_003940825.1_ASM394082v1_genomic.fna/checkm_result
[2024-01-24 15:04:35,708] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:35,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:35,730] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:35,730] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:35,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003940825.1_ASM394082v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:35,731] [INFO] Task started: Blastn
[2024-01-24 15:04:35,731] [INFO] Running command: blastn -query GCF_003940825.1_ASM394082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27c93815-937b-44ed-b0b9-0d48406bc900/dqc_reference/reference_markers_gtdb.fasta -out GCF_003940825.1_ASM394082v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:37,293] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:37,297] [INFO] Selected 22 target genomes.
[2024-01-24 15:04:37,297] [INFO] Target genome list was writen to GCF_003940825.1_ASM394082v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:37,316] [INFO] Task started: fastANI
[2024-01-24 15:04:37,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg45cc70a6-bbf8-4228-b867-3535f549c151/GCF_003940825.1_ASM394082v1_genomic.fna.gz --refList GCF_003940825.1_ASM394082v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003940825.1_ASM394082v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:05:12,622] [INFO] Task succeeded: fastANI
[2024-01-24 15:05:12,645] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:05:12,646] [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_003231305.1	s__Pseudomonas_E sichuanensis	96.2454	1663	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	conclusive
GCF_015354575.1	s__Pseudomonas_E sp015354575	90.1468	1542	2016	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_016861355.1	s__Pseudomonas_E sp001259595	89.1603	1489	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	95.65	95.59	0.90	0.88	5	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	88.9933	1450	2016	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_003205295.1	s__Pseudomonas_E mosselii_B	88.9664	1457	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
GCF_000026105.1	s__Pseudomonas_E entomophila	88.9038	1536	2016	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_019139675.1	s__Pseudomonas_E sp019139675	88.8857	1441	2016	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_018417595.1	s__Pseudomonas_E entomophila_C	88.8565	1517	2016	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_000621225.1	s__Pseudomonas_E mosselii	88.7949	1455	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
GCF_900110655.1	s__Pseudomonas_E soli	88.6822	1404	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.13	95.09	0.90	0.88	23	-
GCF_004519305.1	s__Pseudomonas_E sp004519305	88.6291	1390	2016	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_011752525.1	s__Pseudomonas_E sp011752525	88.1862	1389	2016	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_009391885.1	s__Pseudomonas_E sp009391885	86.9779	1422	2016	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_000282535.1	s__Pseudomonas_E sp000282535	86.9621	1243	2016	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_009932335.1	s__Pseudomonas_E asiatica	86.9312	1397	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	-
GCF_002094795.1	s__Pseudomonas_E putida_K	86.5468	1290	2016	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_013179515.1	s__Pseudomonas_E sp013179515	86.3204	1202	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.82	0.82	2	-
GCF_005080685.1	s__Pseudomonas_E putida_V	86.3023	1375	2016	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_000730605.1	s__Pseudomonas_E monteilii	86.2726	1345	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.80	95.46	0.86	0.79	45	-
GCF_003671955.1	s__Pseudomonas_E hunanensis	85.91	1347	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.33	95.26	0.86	0.79	88	-
GCF_003231275.1	s__Pseudomonas_E huaxiensis	83.8002	1268	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.93	95.93	0.85	0.85	2	-
GCF_014694385.1	s__Pseudomonas_E typographi	79.498	699	2016	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.61	99.56	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:05:12,647] [INFO] GTDB search result was written to GCF_003940825.1_ASM394082v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:05:12,648] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:05:12,653] [INFO] DFAST_QC result json was written to GCF_003940825.1_ASM394082v1_genomic.fna/dqc_result.json
[2024-01-24 15:05:12,653] [INFO] DFAST_QC completed!
[2024-01-24 15:05:12,654] [INFO] Total running time: 0h2m49s