[2023-03-17 08:31:46,166] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:31:46,167] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:31:46,167] [INFO] DQC Reference Directory: /var/lib/cwl/stg28105a3e-df22-4cbf-abde-36be8ce7297e/dqc_reference
[2023-03-17 08:31:47,408] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:31:47,409] [INFO] Task started: Prodigal
[2023-03-17 08:31:47,409] [INFO] Running command: cat /var/lib/cwl/stgf2dbfc1e-8b62-47eb-825b-3538afba1443/OceanDNA-b38636.fa | prodigal -d OceanDNA-b38636/cds.fna -a OceanDNA-b38636/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:31:59,353] [INFO] Task succeeded: Prodigal
[2023-03-17 08:31:59,353] [INFO] Task started: HMMsearch
[2023-03-17 08:31:59,353] [INFO] Running command: hmmsearch --tblout OceanDNA-b38636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28105a3e-df22-4cbf-abde-36be8ce7297e/dqc_reference/reference_markers.hmm OceanDNA-b38636/protein.faa > /dev/null
[2023-03-17 08:31:59,564] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:31:59,564] [INFO] Found 6/6 markers.
[2023-03-17 08:31:59,579] [INFO] Query marker FASTA was written to OceanDNA-b38636/markers.fasta
[2023-03-17 08:31:59,580] [INFO] Task started: Blastn
[2023-03-17 08:31:59,580] [INFO] Running command: blastn -query OceanDNA-b38636/markers.fasta -db /var/lib/cwl/stg28105a3e-df22-4cbf-abde-36be8ce7297e/dqc_reference/reference_markers.fasta -out OceanDNA-b38636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:32:00,484] [INFO] Task succeeded: Blastn
[2023-03-17 08:32:00,485] [INFO] Selected 17 target genomes.
[2023-03-17 08:32:00,485] [INFO] Target genome list was writen to OceanDNA-b38636/target_genomes.txt
[2023-03-17 08:32:00,890] [INFO] Task started: fastANI
[2023-03-17 08:32:00,890] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2dbfc1e-8b62-47eb-825b-3538afba1443/OceanDNA-b38636.fa --refList OceanDNA-b38636/target_genomes.txt --output OceanDNA-b38636/fastani_result.tsv --threads 1
[2023-03-17 08:32:11,171] [INFO] Task succeeded: fastANI
[2023-03-17 08:32:11,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28105a3e-df22-4cbf-abde-36be8ce7297e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:32:11,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28105a3e-df22-4cbf-abde-36be8ce7297e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:32:11,354] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:32:11,355] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:32:11,355] [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 celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	82.2175	398	739	95	below_threshold
Psychrobacter pacificensis	strain=DSM 23406	GCA_900101915.1	112002	112002	type	True	80.4712	339	739	95	below_threshold
Psychrobacter halodurans	strain=F2608	GCA_017498075.1	2818439	2818439	type	True	79.6098	379	739	95	below_threshold
Psychrobacter coccoides	strain=F1192	GCA_017498085.1	2818440	2818440	type	True	78.9474	294	739	95	below_threshold
Psychrobacter faecalis	strain=DSM 14664	GCA_016107575.1	180588	180588	type	True	78.8654	355	739	95	below_threshold
Psychrobacter communis	strain=Sa4CVA2	GCA_014836505.1	2762238	2762238	type	True	78.6968	330	739	95	below_threshold
Psychrobacter glaciei	strain=KCTC 42280	GCA_014652895.1	619771	619771	type	True	78.5668	335	739	95	below_threshold
Psychrobacter aquimaris	strain=DSM 16329	GCA_016107525.1	292733	292733	type	True	78.5002	303	739	95	below_threshold
Psychrobacter namhaensis	strain=DSM 16330	GCA_016107545.1	292734	292734	type	True	78.4982	290	739	95	below_threshold
Psychrobacter luti	strain=CECT 5885	GCA_014192115.1	198481	198481	type	True	78.493	303	739	95	below_threshold
Psychrobacter immobilis	strain=DSM 7229	GCA_003148585.1	498	498	suspected-type	True	78.4381	314	739	95	below_threshold
Psychrobacter cibarius	strain=DSM 16327	GCA_016107535.1	282669	282669	type	True	78.3606	311	739	95	below_threshold
Psychrobacter arcticus	strain=273-4	GCA_000012305.1	334543	334543	type	True	78.3077	273	739	95	below_threshold
Psychrobacter fozii	strain=CECT 5889	GCA_003217155.1	198480	198480	type	True	78.0979	292	739	95	below_threshold
Psychrobacter cryohalolentis	strain=K5	GCA_000013905.1	330922	330922	type	True	78.032	307	739	95	below_threshold
Psychrobacter frigidicola	strain=ACAM 304	GCA_007997305.1	45611	45611	type	True	77.887	258	739	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:32:11,355] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38636/tc_result.tsv
[2023-03-17 08:32:11,355] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:32:11,355] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:32:11,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28105a3e-df22-4cbf-abde-36be8ce7297e/dqc_reference/checkm_data
[2023-03-17 08:32:11,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:32:11,504] [INFO] Task started: CheckM
[2023-03-17 08:32:11,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38636/checkm_input OceanDNA-b38636/checkm_result
[2023-03-17 08:32:51,763] [INFO] Task succeeded: CheckM
[2023-03-17 08:32:51,764] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:32:51,766] [INFO] ===== Completeness check finished =====
[2023-03-17 08:32:51,766] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:32:51,766] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38636/markers.fasta)
[2023-03-17 08:32:51,787] [INFO] Task started: Blastn
[2023-03-17 08:32:51,788] [INFO] Running command: blastn -query OceanDNA-b38636/markers.fasta -db /var/lib/cwl/stg28105a3e-df22-4cbf-abde-36be8ce7297e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:32:53,449] [INFO] Task succeeded: Blastn
[2023-03-17 08:32:53,450] [INFO] Selected 25 target genomes.
[2023-03-17 08:32:53,450] [INFO] Target genome list was writen to OceanDNA-b38636/target_genomes_gtdb.txt
[2023-03-17 08:32:54,527] [INFO] Task started: fastANI
[2023-03-17 08:32:54,527] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2dbfc1e-8b62-47eb-825b-3538afba1443/OceanDNA-b38636.fa --refList OceanDNA-b38636/target_genomes_gtdb.txt --output OceanDNA-b38636/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:33:10,891] [INFO] Task succeeded: fastANI
[2023-03-17 08:33:10,906] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:33:10,906] [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_904846685.1	s__Psychrobacter sp000511655	97.741	701	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.68	97.54	0.87	0.80	6	conclusive
GCF_016107555.1	s__Psychrobacter celer	82.2577	396	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.12	95.68	0.88	0.85	9	-
GCF_900101915.1	s__Psychrobacter pacificensis	80.5048	338	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2282	98.35	97.54	0.93	0.90	8	-
GCF_904846415.1	s__Psychrobacter piscatorii_A	79.155	321	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846145.1	s__Psychrobacter immobilis_G	78.8565	355	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107575.1	s__Psychrobacter faecalis	78.8458	356	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.81	95.77	0.89	0.85	16	-
GCF_002836735.1	s__Psychrobacter sp002836735	78.8146	290	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	95.08	95.08	0.86	0.86	2	-
GCF_904846155.1	s__Psychrobacter fulvigenes	78.6473	337	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.04	97.04	0.87	0.87	2	-
GCF_904846345.1	s__Psychrobacter maritimus	78.5435	343	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	96.41	96.16	0.91	0.90	6	-
GCF_003350005.1	s__Psychrobacter proteolyticus_A	78.5324	278	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	99.98	99.95	0.99	0.99	4	-
GCF_014192115.1	s__Psychrobacter luti	78.5012	304	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001435845.1	s__Psychrobacter sp001435845	78.4868	297	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846185.1	s__Psychrobacter immobilis_B	78.4547	316	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3523	99.90	99.90	0.97	0.97	2	-
GCF_904846075.1	s__Psychrobacter glacincola_C	78.3818	314	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	96.53	96.53	0.88	0.88	2	-
GCF_900163785.1	s__Psychrobacter alimentarius	78.3486	293	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.11	97.08	0.93	0.93	3	-
GCF_016107535.1	s__Psychrobacter cibarius	78.3484	312	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.3915	99.97	99.97	0.99	0.99	2	-
GCF_904846615.1	s__Psychrobacter sp000586455	78.2996	326	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4083	99.93	99.93	1.00	1.00	2	-
GCF_904846285.1	s__Psychrobacter immobilis_D	78.2388	323	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369115.1	s__Psychrobacter sp008369115	78.1847	291	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000586475.1	s__Psychrobacter sp000586475	78.1818	322	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.2677	98.16	96.39	0.95	0.90	3	-
GCF_001606025.1	s__Psychrobacter alimentarius_A	78.1559	296	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	98.60	97.20	0.95	0.90	3	-
GCA_001411745.2	s__Psychrobacter glacincola_A	78.1356	320	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	96.4049	N/A	N/A	N/A	N/A	1	-
GCF_000013905.1	s__Psychrobacter cryohalolentis	78.0396	307	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.64	96.60	0.93	0.89	9	-
GCF_001298525.1	s__Psychrobacter urativorans_A	77.9226	249	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904846695.1	s__Psychrobacter urativorans_C	77.8587	272	739	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:33:10,907] [INFO] GTDB search result was written to OceanDNA-b38636/result_gtdb.tsv
[2023-03-17 08:33:10,907] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:33:10,909] [INFO] DFAST_QC result json was written to OceanDNA-b38636/dqc_result.json
[2023-03-17 08:33:10,909] [INFO] DFAST_QC completed!
[2023-03-17 08:33:10,909] [INFO] Total running time: 0h1m25s