[2023-03-19 02:20:31,371] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:20:31,371] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:20:31,371] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cace122-5d05-497d-84d3-e7c1dd7097c0/dqc_reference
[2023-03-19 02:20:32,468] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:20:32,469] [INFO] Task started: Prodigal
[2023-03-19 02:20:32,469] [INFO] Running command: cat /var/lib/cwl/stg888d3d59-c4c7-4008-a99b-ce0901666b41/OceanDNA-b38602.fa | prodigal -d OceanDNA-b38602/cds.fna -a OceanDNA-b38602/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:20:46,575] [INFO] Task succeeded: Prodigal
[2023-03-19 02:20:46,575] [INFO] Task started: HMMsearch
[2023-03-19 02:20:46,575] [INFO] Running command: hmmsearch --tblout OceanDNA-b38602/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cace122-5d05-497d-84d3-e7c1dd7097c0/dqc_reference/reference_markers.hmm OceanDNA-b38602/protein.faa > /dev/null
[2023-03-19 02:20:46,749] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:20:46,749] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg888d3d59-c4c7-4008-a99b-ce0901666b41/OceanDNA-b38602.fa]
[2023-03-19 02:20:46,765] [INFO] Query marker FASTA was written to OceanDNA-b38602/markers.fasta
[2023-03-19 02:20:46,766] [INFO] Task started: Blastn
[2023-03-19 02:20:46,766] [INFO] Running command: blastn -query OceanDNA-b38602/markers.fasta -db /var/lib/cwl/stg1cace122-5d05-497d-84d3-e7c1dd7097c0/dqc_reference/reference_markers.fasta -out OceanDNA-b38602/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:20:47,338] [INFO] Task succeeded: Blastn
[2023-03-19 02:20:47,339] [INFO] Selected 14 target genomes.
[2023-03-19 02:20:47,339] [INFO] Target genome list was writen to OceanDNA-b38602/target_genomes.txt
[2023-03-19 02:20:47,358] [INFO] Task started: fastANI
[2023-03-19 02:20:47,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg888d3d59-c4c7-4008-a99b-ce0901666b41/OceanDNA-b38602.fa --refList OceanDNA-b38602/target_genomes.txt --output OceanDNA-b38602/fastani_result.tsv --threads 1
[2023-03-19 02:20:55,825] [INFO] Task succeeded: fastANI
[2023-03-19 02:20:55,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cace122-5d05-497d-84d3-e7c1dd7097c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:20:55,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cace122-5d05-497d-84d3-e7c1dd7097c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:20:55,834] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:20:55,834] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:20:55,834] [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
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	92.2616	718	843	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	82.1238	589	843	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	81.0823	584	843	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	80.9054	566	843	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	80.8843	568	843	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	80.7815	556	843	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	80.7	553	843	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	80.5099	555	843	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	80.3443	467	843	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	79.6797	482	843	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	79.4647	457	843	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	79.3263	445	843	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:20:55,834] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38602/tc_result.tsv
[2023-03-19 02:20:55,835] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:20:55,835] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:20:55,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cace122-5d05-497d-84d3-e7c1dd7097c0/dqc_reference/checkm_data
[2023-03-19 02:20:55,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:20:55,840] [INFO] Task started: CheckM
[2023-03-19 02:20:55,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38602/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38602/checkm_input OceanDNA-b38602/checkm_result
[2023-03-19 02:21:34,224] [INFO] Task succeeded: CheckM
[2023-03-19 02:21:34,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.65%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:21:34,302] [INFO] ===== Completeness check finished =====
[2023-03-19 02:21:34,302] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:21:34,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38602/markers.fasta)
[2023-03-19 02:21:34,303] [INFO] Task started: Blastn
[2023-03-19 02:21:34,303] [INFO] Running command: blastn -query OceanDNA-b38602/markers.fasta -db /var/lib/cwl/stg1cace122-5d05-497d-84d3-e7c1dd7097c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38602/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:21:35,204] [INFO] Task succeeded: Blastn
[2023-03-19 02:21:35,206] [INFO] Selected 13 target genomes.
[2023-03-19 02:21:35,206] [INFO] Target genome list was writen to OceanDNA-b38602/target_genomes_gtdb.txt
[2023-03-19 02:21:35,221] [INFO] Task started: fastANI
[2023-03-19 02:21:35,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg888d3d59-c4c7-4008-a99b-ce0901666b41/OceanDNA-b38602.fa --refList OceanDNA-b38602/target_genomes_gtdb.txt --output OceanDNA-b38602/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:21:44,293] [INFO] Task succeeded: fastANI
[2023-03-19 02:21:44,301] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:21:44,301] [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_904846415.1	s__Psychrobacter piscatorii_A	94.2995	743	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444505.1	s__Psychrobacter piscatorii	92.7265	712	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	97.27	96.69	0.93	0.91	3	-
GCF_900101915.1	s__Psychrobacter pacificensis	92.274	717	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	-
GCF_904846235.1	s__Psychrobacter immobilis_C	84.7044	672	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836735.1	s__Psychrobacter sp002836735	84.7022	678	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_009812035.1	s__Psychrobacter nivimaris_A	84.6282	687	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000586435.1	s__Psychrobacter sp000586435	84.554	675	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846645.1	s__Psychrobacter sp904846645	84.5171	676	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435845.1	s__Psychrobacter sp001435845	84.502	693	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846625.1	s__Psychrobacter sp000586415	84.4997	687	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.91	99.91	1.00	1.00	2	-
GCF_014770435.1	s__Psychrobacter sp014770435	84.4013	680	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277735.1	s__Psychrobacter sp015277735	82.4328	652	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.26	95.15	0.92	0.92	3	-
GCF_900163785.1	s__Psychrobacter alimentarius	82.0311	555	843	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.11	97.08	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2023-03-19 02:21:44,302] [INFO] GTDB search result was written to OceanDNA-b38602/result_gtdb.tsv
[2023-03-19 02:21:44,304] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:21:44,306] [INFO] DFAST_QC result json was written to OceanDNA-b38602/dqc_result.json
[2023-03-19 02:21:44,306] [INFO] DFAST_QC completed!
[2023-03-19 02:21:44,306] [INFO] Total running time: 0h1m13s