[2023-03-17 04:15:15,032] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:15,032] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:15,032] [INFO] DQC Reference Directory: /var/lib/cwl/stgddda016d-ac2d-4e08-8e5b-2146559e9267/dqc_reference
[2023-03-17 04:15:16,759] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,760] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,760] [INFO] Running command: cat /var/lib/cwl/stg4e80cbde-4c24-4a75-800f-a22d11d7c0a4/OceanDNA-b35084.fa | prodigal -d OceanDNA-b35084/cds.fna -a OceanDNA-b35084/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:32,763] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:32,763] [INFO] Task started: HMMsearch
[2023-03-17 04:15:32,763] [INFO] Running command: hmmsearch --tblout OceanDNA-b35084/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddda016d-ac2d-4e08-8e5b-2146559e9267/dqc_reference/reference_markers.hmm OceanDNA-b35084/protein.faa > /dev/null
[2023-03-17 04:15:32,994] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:32,994] [INFO] Found 6/6 markers.
[2023-03-17 04:15:33,018] [INFO] Query marker FASTA was written to OceanDNA-b35084/markers.fasta
[2023-03-17 04:15:33,018] [INFO] Task started: Blastn
[2023-03-17 04:15:33,018] [INFO] Running command: blastn -query OceanDNA-b35084/markers.fasta -db /var/lib/cwl/stgddda016d-ac2d-4e08-8e5b-2146559e9267/dqc_reference/reference_markers.fasta -out OceanDNA-b35084/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:33,671] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:33,672] [INFO] Selected 15 target genomes.
[2023-03-17 04:15:33,672] [INFO] Target genome list was writen to OceanDNA-b35084/target_genomes.txt
[2023-03-17 04:15:33,680] [INFO] Task started: fastANI
[2023-03-17 04:15:33,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e80cbde-4c24-4a75-800f-a22d11d7c0a4/OceanDNA-b35084.fa --refList OceanDNA-b35084/target_genomes.txt --output OceanDNA-b35084/fastani_result.tsv --threads 1
[2023-03-17 04:15:46,697] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:46,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddda016d-ac2d-4e08-8e5b-2146559e9267/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:46,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddda016d-ac2d-4e08-8e5b-2146559e9267/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:46,706] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:46,706] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:46,706] [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
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	94.4843	946	1037	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	93.3819	948	1037	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	89.8421	873	1037	95	below_threshold
Pseudoalteromonas aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	86.9195	781	1037	95	below_threshold
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	85.1904	885	1037	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	85.1754	883	1037	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	85.0871	877	1037	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	83.279	753	1037	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	82.888	649	1037	95	below_threshold
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	82.6069	650	1037	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	80.5995	461	1037	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	80.5379	487	1037	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	77.7358	157	1037	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	76.5143	57	1037	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:46,706] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35084/tc_result.tsv
[2023-03-17 04:15:46,706] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:46,706] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:46,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddda016d-ac2d-4e08-8e5b-2146559e9267/dqc_reference/checkm_data
[2023-03-17 04:15:46,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:46,712] [INFO] Task started: CheckM
[2023-03-17 04:15:46,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35084/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35084/checkm_input OceanDNA-b35084/checkm_result
[2023-03-17 04:16:28,530] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:28,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:28,533] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:28,533] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:28,533] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35084/markers.fasta)
[2023-03-17 04:16:28,533] [INFO] Task started: Blastn
[2023-03-17 04:16:28,533] [INFO] Running command: blastn -query OceanDNA-b35084/markers.fasta -db /var/lib/cwl/stgddda016d-ac2d-4e08-8e5b-2146559e9267/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35084/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:29,561] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:29,561] [INFO] Selected 8 target genomes.
[2023-03-17 04:16:29,562] [INFO] Target genome list was writen to OceanDNA-b35084/target_genomes_gtdb.txt
[2023-03-17 04:16:29,616] [INFO] Task started: fastANI
[2023-03-17 04:16:29,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e80cbde-4c24-4a75-800f-a22d11d7c0a4/OceanDNA-b35084.fa --refList OceanDNA-b35084/target_genomes_gtdb.txt --output OceanDNA-b35084/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:37,353] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:37,359] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:16:37,359] [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_001974875.1	s__Pseudoalteromonas sp001974875	98.0873	1009	1037	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	conclusive
GCF_000238395.3	s__Pseudoalteromonas arctica	94.4868	946	1037	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCA_000814675.1	s__Pseudoalteromonas distincta	93.3819	948	1037	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	92.6817	911	1037	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	92.4935	914	1037	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000239855.1	s__Pseudoalteromonas sp000239855	91.0388	834	1037	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	89.8415	873	1037	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	81.8169	454	1037	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:37,359] [INFO] GTDB search result was written to OceanDNA-b35084/result_gtdb.tsv
[2023-03-17 04:16:37,359] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:37,360] [INFO] DFAST_QC result json was written to OceanDNA-b35084/dqc_result.json
[2023-03-17 04:16:37,360] [INFO] DFAST_QC completed!
[2023-03-17 04:16:37,360] [INFO] Total running time: 0h1m22s