[2023-03-19 00:01:03,428] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,428] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,428] [INFO] DQC Reference Directory: /var/lib/cwl/stga6112bd6-1b4d-49e3-8658-62617f2b0ec0/dqc_reference
[2023-03-19 00:01:04,672] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,672] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,672] [INFO] Running command: cat /var/lib/cwl/stg61747878-3880-4549-83ca-60fe2f6870e0/OceanDNA-b41228.fa | prodigal -d OceanDNA-b41228/cds.fna -a OceanDNA-b41228/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:23,568] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:23,568] [INFO] Task started: HMMsearch
[2023-03-19 00:01:23,568] [INFO] Running command: hmmsearch --tblout OceanDNA-b41228/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6112bd6-1b4d-49e3-8658-62617f2b0ec0/dqc_reference/reference_markers.hmm OceanDNA-b41228/protein.faa > /dev/null
[2023-03-19 00:01:23,832] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:23,832] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg61747878-3880-4549-83ca-60fe2f6870e0/OceanDNA-b41228.fa]
[2023-03-19 00:01:23,857] [INFO] Query marker FASTA was written to OceanDNA-b41228/markers.fasta
[2023-03-19 00:01:23,857] [INFO] Task started: Blastn
[2023-03-19 00:01:23,857] [INFO] Running command: blastn -query OceanDNA-b41228/markers.fasta -db /var/lib/cwl/stga6112bd6-1b4d-49e3-8658-62617f2b0ec0/dqc_reference/reference_markers.fasta -out OceanDNA-b41228/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:24,575] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:24,576] [INFO] Selected 14 target genomes.
[2023-03-19 00:01:24,576] [INFO] Target genome list was writen to OceanDNA-b41228/target_genomes.txt
[2023-03-19 00:01:24,584] [INFO] Task started: fastANI
[2023-03-19 00:01:24,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg61747878-3880-4549-83ca-60fe2f6870e0/OceanDNA-b41228.fa --refList OceanDNA-b41228/target_genomes.txt --output OceanDNA-b41228/fastani_result.tsv --threads 1
[2023-03-19 00:01:37,022] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:37,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6112bd6-1b4d-49e3-8658-62617f2b0ec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:37,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6112bd6-1b4d-49e3-8658-62617f2b0ec0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:37,032] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:37,032] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:01:37,032] [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 peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	85.2344	773	955	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	85.2225	763	955	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	84.9325	734	955	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	81.2248	579	955	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	81.1909	563	955	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	80.9853	564	955	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	80.5173	549	955	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	80.3542	577	955	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	80.1798	515	955	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	80.1562	576	955	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	79.6271	484	955	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	78.8572	323	955	95	below_threshold
Pseudomonas marincola	strain=JCM 14761	GCA_900116605.1	437900	437900	type	True	78.7491	409	955	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	78.5331	336	955	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:01:37,032] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41228/tc_result.tsv
[2023-03-19 00:01:37,032] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:37,032] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:37,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6112bd6-1b4d-49e3-8658-62617f2b0ec0/dqc_reference/checkm_data
[2023-03-19 00:01:37,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:37,039] [INFO] Task started: CheckM
[2023-03-19 00:01:37,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41228/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41228/checkm_input OceanDNA-b41228/checkm_result
[2023-03-19 00:02:25,615] [INFO] Task succeeded: CheckM
[2023-03-19 00:02:25,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:02:25,618] [INFO] ===== Completeness check finished =====
[2023-03-19 00:02:25,619] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:02:25,619] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41228/markers.fasta)
[2023-03-19 00:02:25,619] [INFO] Task started: Blastn
[2023-03-19 00:02:25,619] [INFO] Running command: blastn -query OceanDNA-b41228/markers.fasta -db /var/lib/cwl/stga6112bd6-1b4d-49e3-8658-62617f2b0ec0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41228/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:02:26,861] [INFO] Task succeeded: Blastn
[2023-03-19 00:02:26,862] [INFO] Selected 11 target genomes.
[2023-03-19 00:02:26,862] [INFO] Target genome list was writen to OceanDNA-b41228/target_genomes_gtdb.txt
[2023-03-19 00:02:26,905] [INFO] Task started: fastANI
[2023-03-19 00:02:26,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg61747878-3880-4549-83ca-60fe2f6870e0/OceanDNA-b41228.fa --refList OceanDNA-b41228/target_genomes_gtdb.txt --output OceanDNA-b41228/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:36,631] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:36,638] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:02:36,638] [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_004920405.1	s__Pseudomonas_E leptonychotis	97.7677	892	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002840155.1	s__Pseudomonas_E sp002840155	86.3422	813	955	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_018827205.1	s__Pseudomonas_E sp018827205	85.6494	760	955	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_900099645.1	s__Pseudomonas_E peli	85.212	775	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCF_900113745.1	s__Pseudomonas_E guineae	84.9437	733	955	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_018816095.1	s__Pseudomonas_E sp018816095	84.4195	656	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCA_017886405.1	s__Pseudomonas_E sp017886405	83.3048	505	955	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_002354655.1	s__Pseudomonas_E sp002354655	82.1404	655	955	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_013184545.1	s__Pseudomonas_E sp013184545	81.2084	580	955	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	81.0403	584	955	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	81.0034	563	955	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:36,639] [INFO] GTDB search result was written to OceanDNA-b41228/result_gtdb.tsv
[2023-03-19 00:02:36,639] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:36,640] [INFO] DFAST_QC result json was written to OceanDNA-b41228/dqc_result.json
[2023-03-19 00:02:36,640] [INFO] DFAST_QC completed!
[2023-03-19 00:02:36,640] [INFO] Total running time: 0h1m33s