[2023-03-14 11:14:12,736] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,736] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg98851480-23fb-4ce3-b309-f8032efb8d49/dqc_reference
[2023-03-14 11:14:14,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,202] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,203] [INFO] Running command: cat /var/lib/cwl/stgb7862553-30a9-4b56-9505-196d8725ccff/OceanDNA-b41214.fa | prodigal -d OceanDNA-b41214/cds.fna -a OceanDNA-b41214/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:42,821] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:42,822] [INFO] Task started: HMMsearch
[2023-03-14 11:14:42,822] [INFO] Running command: hmmsearch --tblout OceanDNA-b41214/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98851480-23fb-4ce3-b309-f8032efb8d49/dqc_reference/reference_markers.hmm OceanDNA-b41214/protein.faa > /dev/null
[2023-03-14 11:14:43,101] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:43,102] [INFO] Found 6/6 markers.
[2023-03-14 11:14:43,135] [INFO] Query marker FASTA was written to OceanDNA-b41214/markers.fasta
[2023-03-14 11:14:43,136] [INFO] Task started: Blastn
[2023-03-14 11:14:43,136] [INFO] Running command: blastn -query OceanDNA-b41214/markers.fasta -db /var/lib/cwl/stg98851480-23fb-4ce3-b309-f8032efb8d49/dqc_reference/reference_markers.fasta -out OceanDNA-b41214/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:43,995] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:43,995] [INFO] Selected 18 target genomes.
[2023-03-14 11:14:43,996] [INFO] Target genome list was writen to OceanDNA-b41214/target_genomes.txt
[2023-03-14 11:14:44,007] [INFO] Task started: fastANI
[2023-03-14 11:14:44,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7862553-30a9-4b56-9505-196d8725ccff/OceanDNA-b41214.fa --refList OceanDNA-b41214/target_genomes.txt --output OceanDNA-b41214/fastani_result.tsv --threads 1
[2023-03-14 11:15:03,649] [INFO] Task succeeded: fastANI
[2023-03-14 11:15:03,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98851480-23fb-4ce3-b309-f8032efb8d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:15:03,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98851480-23fb-4ce3-b309-f8032efb8d49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:15:03,660] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:15:03,660] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:15:03,660] [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 tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	92.2211	1136	1531	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	91.0595	1125	1531	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	85.9261	1056	1531	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.5809	907	1531	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	83.6746	993	1531	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	82.3056	826	1531	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.2289	767	1531	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	81.9143	760	1531	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	81.8802	773	1531	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	81.6707	769	1531	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.39	715	1531	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	81.3024	640	1531	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	80.9679	698	1531	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	80.9294	712	1531	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	80.8041	574	1531	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	80.7284	691	1531	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	80.6884	685	1531	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	80.1479	650	1531	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:15:03,660] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41214/tc_result.tsv
[2023-03-14 11:15:03,661] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:15:03,661] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:15:03,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98851480-23fb-4ce3-b309-f8032efb8d49/dqc_reference/checkm_data
[2023-03-14 11:15:03,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:15:03,669] [INFO] Task started: CheckM
[2023-03-14 11:15:03,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41214/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41214/checkm_input OceanDNA-b41214/checkm_result
[2023-03-14 11:16:13,578] [INFO] Task succeeded: CheckM
[2023-03-14 11:16:13,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.10%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 11:16:13,582] [INFO] ===== Completeness check finished =====
[2023-03-14 11:16:13,582] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:16:13,583] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41214/markers.fasta)
[2023-03-14 11:16:13,584] [INFO] Task started: Blastn
[2023-03-14 11:16:13,584] [INFO] Running command: blastn -query OceanDNA-b41214/markers.fasta -db /var/lib/cwl/stg98851480-23fb-4ce3-b309-f8032efb8d49/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41214/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:16:15,509] [INFO] Task succeeded: Blastn
[2023-03-14 11:16:15,510] [INFO] Selected 16 target genomes.
[2023-03-14 11:16:15,510] [INFO] Target genome list was writen to OceanDNA-b41214/target_genomes_gtdb.txt
[2023-03-14 11:16:15,544] [INFO] Task started: fastANI
[2023-03-14 11:16:15,544] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7862553-30a9-4b56-9505-196d8725ccff/OceanDNA-b41214.fa --refList OceanDNA-b41214/target_genomes_gtdb.txt --output OceanDNA-b41214/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:16:34,035] [INFO] Task succeeded: fastANI
[2023-03-14 11:16:34,045] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:16:34,045] [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_013184545.1	s__Pseudomonas_E sp013184545	92.2366	1135	1531	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_900115555.1	s__Pseudomonas_E borbori	91.0301	1127	1531	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_002025205.1	s__Pseudomonas_E sp002025205	89.1524	1098	1531	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_900100495.1	s__Pseudomonas_E benzenivorans	85.8922	1060	1531	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_018398425.1	s__Pseudomonas_E lalucatii	84.5546	910	1531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	84.2402	953	1531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCF_007993865.1	s__Pseudomonas_E sp007993865	83.8278	972	1531	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_000498575.2	s__Pseudomonas_E taeanensis	83.6935	991	1531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840155.1	s__Pseudomonas_E sp002840155	82.8427	837	1531	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_004327355.1	s__Pseudomonas_E dryadis	82.0562	789	1531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	81.8055	736	1531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_016901015.1	s__Pseudomonas_E sp016901015	81.4268	711	1531	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_001839655.1	s__Pseudomonas_E argentinensis_B	81.2478	713	1531	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_000213805.1	s__Pseudomonas_E fulva_B	81.2047	702	1531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCF_002286785.1	s__Pseudomonas_M sp002286785	80.9162	812	1531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001579805.1	s__Pseudomonas_E azotoformans_A	79.1155	587	1531	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.75	96.24	0.87	0.84	8	-
--------------------------------------------------------------------------------
[2023-03-14 11:16:34,045] [INFO] GTDB search result was written to OceanDNA-b41214/result_gtdb.tsv
[2023-03-14 11:16:34,045] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:16:34,047] [INFO] DFAST_QC result json was written to OceanDNA-b41214/dqc_result.json
[2023-03-14 11:16:34,047] [INFO] DFAST_QC completed!
[2023-03-14 11:16:34,047] [INFO] Total running time: 0h2m21s