[2023-03-15 03:14:16,370] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,370] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg2373c8bb-4d4c-4ad3-bc32-f8a53c8e6a76/dqc_reference
[2023-03-15 03:14:17,549] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,549] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,549] [INFO] Running command: cat /var/lib/cwl/stg7499e0d1-4ef8-4496-8a27-639dd7bfd070/OceanDNA-b38604.fa | prodigal -d OceanDNA-b38604/cds.fna -a OceanDNA-b38604/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:31,019] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:31,020] [INFO] Task started: HMMsearch
[2023-03-15 03:14:31,020] [INFO] Running command: hmmsearch --tblout OceanDNA-b38604/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2373c8bb-4d4c-4ad3-bc32-f8a53c8e6a76/dqc_reference/reference_markers.hmm OceanDNA-b38604/protein.faa > /dev/null
[2023-03-15 03:14:31,245] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:31,245] [INFO] Found 6/6 markers.
[2023-03-15 03:14:31,264] [INFO] Query marker FASTA was written to OceanDNA-b38604/markers.fasta
[2023-03-15 03:14:31,264] [INFO] Task started: Blastn
[2023-03-15 03:14:31,264] [INFO] Running command: blastn -query OceanDNA-b38604/markers.fasta -db /var/lib/cwl/stg2373c8bb-4d4c-4ad3-bc32-f8a53c8e6a76/dqc_reference/reference_markers.fasta -out OceanDNA-b38604/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:31,851] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:31,852] [INFO] Selected 16 target genomes.
[2023-03-15 03:14:31,853] [INFO] Target genome list was writen to OceanDNA-b38604/target_genomes.txt
[2023-03-15 03:14:31,862] [INFO] Task started: fastANI
[2023-03-15 03:14:31,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg7499e0d1-4ef8-4496-8a27-639dd7bfd070/OceanDNA-b38604.fa --refList OceanDNA-b38604/target_genomes.txt --output OceanDNA-b38604/fastani_result.tsv --threads 1
[2023-03-15 03:14:41,456] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:41,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2373c8bb-4d4c-4ad3-bc32-f8a53c8e6a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:41,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2373c8bb-4d4c-4ad3-bc32-f8a53c8e6a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:41,465] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:41,465] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:14:41,465] [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	88.8716	600	756	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	80.5474	469	756	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	80.2903	431	756	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	80.1508	394	756	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	79.9652	452	756	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	79.9253	458	756	95	below_threshold
Psychrobacter aquaticus	strain=CMS 56	GCA_000471625.1	248452	248452	type	True	79.8679	460	756	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	79.8443	445	756	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	79.7927	445	756	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	79.4396	372	756	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	79.0473	380	756	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	79.0187	363	756	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	78.9987	337	756	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	78.9837	383	756	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:14:41,465] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38604/tc_result.tsv
[2023-03-15 03:14:41,465] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:41,465] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:41,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2373c8bb-4d4c-4ad3-bc32-f8a53c8e6a76/dqc_reference/checkm_data
[2023-03-15 03:14:41,466] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:41,471] [INFO] Task started: CheckM
[2023-03-15 03:14:41,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38604/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38604/checkm_input OceanDNA-b38604/checkm_result
[2023-03-15 03:15:19,279] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:19,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:19,282] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:19,282] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:19,282] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38604/markers.fasta)
[2023-03-15 03:15:19,282] [INFO] Task started: Blastn
[2023-03-15 03:15:19,283] [INFO] Running command: blastn -query OceanDNA-b38604/markers.fasta -db /var/lib/cwl/stg2373c8bb-4d4c-4ad3-bc32-f8a53c8e6a76/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38604/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:20,203] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:20,204] [INFO] Selected 21 target genomes.
[2023-03-15 03:15:20,204] [INFO] Target genome list was writen to OceanDNA-b38604/target_genomes_gtdb.txt
[2023-03-15 03:15:20,223] [INFO] Task started: fastANI
[2023-03-15 03:15:20,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg7499e0d1-4ef8-4496-8a27-639dd7bfd070/OceanDNA-b38604.fa --refList OceanDNA-b38604/target_genomes_gtdb.txt --output OceanDNA-b38604/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:32,590] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:32,602] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:15:32,602] [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_900101915.1	s__Psychrobacter pacificensis	88.8716	600	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	-
GCF_001444505.1	s__Psychrobacter piscatorii	88.5804	597	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	97.27	96.69	0.93	0.91	3	-
GCF_904846415.1	s__Psychrobacter piscatorii_A	86.1303	619	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846235.1	s__Psychrobacter immobilis_C	82.4225	541	756	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	82.243	528	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836715.1	s__Psychrobacter sp002836715	82.1343	523	756	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	82.1337	548	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_013414195.1	s__Psychrobacter sp013414195	82.0882	537	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009812035.1	s__Psychrobacter nivimaris_A	82.0417	557	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350005.1	s__Psychrobacter proteolyticus_A	82.0167	536	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.98	99.95	0.99	0.99	4	-
GCF_015277735.1	s__Psychrobacter sp015277735	81.1265	526	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.26	95.15	0.92	0.92	3	-
GCF_003217155.1	s__Psychrobacter fozii	79.9652	452	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.56	95.06	0.91	0.88	5	-
GCF_000471625.1	s__Psychrobacter aquaticus	79.8733	460	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904846075.1	s__Psychrobacter glacincola_C	79.8231	455	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	96.53	96.53	0.88	0.88	2	-
GCA_018448495.1	s__Psychrobacter sp018448495	79.8052	452	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.24	97.46	97.46	0.95	0.95	2	-
GCA_001411745.2	s__Psychrobacter glacincola_A	79.7485	445	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	N/A	N/A	N/A	N/A	1	-
GCF_904846225.1	s__Psychrobacter immobilis_F	79.6686	454	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014861395.1	s__Psychrobacter sp014861395	79.2387	383	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.67	98.67	0.84	0.84	2	-
GCA_002453355.1	s__Psychrobacter sp002453355	78.7139	352	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846605.1	s__Psychrobacter sp904846605	77.9149	292	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_904846675.1	s__Psychrobacter urativorans_B	77.5322	233	756	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.89	97.89	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:32,602] [INFO] GTDB search result was written to OceanDNA-b38604/result_gtdb.tsv
[2023-03-15 03:15:32,602] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:32,604] [INFO] DFAST_QC result json was written to OceanDNA-b38604/dqc_result.json
[2023-03-15 03:15:32,604] [INFO] DFAST_QC completed!
[2023-03-15 03:15:32,604] [INFO] Total running time: 0h1m16s