[2023-03-16 05:09:10,890] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:09:10,890] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:09:10,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b499b68-9b06-43fc-a8d9-397fd27c6e40/dqc_reference
[2023-03-16 05:09:12,013] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:09:12,013] [INFO] Task started: Prodigal
[2023-03-16 05:09:12,014] [INFO] Running command: cat /var/lib/cwl/stga7a0d2f2-eca4-4f97-b7eb-d03810510e47/OceanDNA-b41496.fa | prodigal -d OceanDNA-b41496/cds.fna -a OceanDNA-b41496/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:09:34,450] [INFO] Task succeeded: Prodigal
[2023-03-16 05:09:34,450] [INFO] Task started: HMMsearch
[2023-03-16 05:09:34,450] [INFO] Running command: hmmsearch --tblout OceanDNA-b41496/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b499b68-9b06-43fc-a8d9-397fd27c6e40/dqc_reference/reference_markers.hmm OceanDNA-b41496/protein.faa > /dev/null
[2023-03-16 05:09:34,659] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:09:34,659] [INFO] Found 6/6 markers.
[2023-03-16 05:09:34,679] [INFO] Query marker FASTA was written to OceanDNA-b41496/markers.fasta
[2023-03-16 05:09:34,680] [INFO] Task started: Blastn
[2023-03-16 05:09:34,680] [INFO] Running command: blastn -query OceanDNA-b41496/markers.fasta -db /var/lib/cwl/stg7b499b68-9b06-43fc-a8d9-397fd27c6e40/dqc_reference/reference_markers.fasta -out OceanDNA-b41496/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:09:35,387] [INFO] Task succeeded: Blastn
[2023-03-16 05:09:35,388] [INFO] Selected 23 target genomes.
[2023-03-16 05:09:35,389] [INFO] Target genome list was writen to OceanDNA-b41496/target_genomes.txt
[2023-03-16 05:09:35,400] [INFO] Task started: fastANI
[2023-03-16 05:09:35,400] [INFO] Running command: fastANI --query /var/lib/cwl/stga7a0d2f2-eca4-4f97-b7eb-d03810510e47/OceanDNA-b41496.fa --refList OceanDNA-b41496/target_genomes.txt --output OceanDNA-b41496/fastani_result.tsv --threads 1
[2023-03-16 05:09:50,101] [INFO] Task succeeded: fastANI
[2023-03-16 05:09:50,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b499b68-9b06-43fc-a8d9-397fd27c6e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:09:50,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b499b68-9b06-43fc-a8d9-397fd27c6e40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:09:50,112] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 05:09:50,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 05:09:50,112] [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
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	97.9687	1114	1214	95	conclusive
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	79.5221	220	1214	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	78.8232	317	1214	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	78.1615	253	1214	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.7211	230	1214	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.8907	133	1214	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	76.6648	65	1214	95	below_threshold
Pseudomonas taeanensis	strain=MS-3	GCA_000498575.2	574962	574962	type	True	76.3751	66	1214	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.2515	80	1214	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	76.1998	53	1214	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	76.1997	69	1214	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	76.1539	69	1214	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	76.1162	63	1214	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.0238	64	1214	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	76.0148	65	1214	95	below_threshold
Marinobacter daqiaonensis	strain=YCSA40	GCA_012070355.1	650891	650891	type	True	75.9971	60	1214	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	75.9385	75	1214	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.9147	76	1214	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	75.8549	78	1214	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:09:50,113] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41496/tc_result.tsv
[2023-03-16 05:09:50,113] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:09:50,113] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:09:50,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b499b68-9b06-43fc-a8d9-397fd27c6e40/dqc_reference/checkm_data
[2023-03-16 05:09:50,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:09:50,120] [INFO] Task started: CheckM
[2023-03-16 05:09:50,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41496/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41496/checkm_input OceanDNA-b41496/checkm_result
[2023-03-16 05:10:45,958] [INFO] Task succeeded: CheckM
[2023-03-16 05:10:45,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:10:45,962] [INFO] ===== Completeness check finished =====
[2023-03-16 05:10:45,962] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:10:45,962] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41496/markers.fasta)
[2023-03-16 05:10:45,963] [INFO] Task started: Blastn
[2023-03-16 05:10:45,963] [INFO] Running command: blastn -query OceanDNA-b41496/markers.fasta -db /var/lib/cwl/stg7b499b68-9b06-43fc-a8d9-397fd27c6e40/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41496/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:10:47,163] [INFO] Task succeeded: Blastn
[2023-03-16 05:10:47,164] [INFO] Selected 19 target genomes.
[2023-03-16 05:10:47,164] [INFO] Target genome list was writen to OceanDNA-b41496/target_genomes_gtdb.txt
[2023-03-16 05:10:47,207] [INFO] Task started: fastANI
[2023-03-16 05:10:47,207] [INFO] Running command: fastANI --query /var/lib/cwl/stga7a0d2f2-eca4-4f97-b7eb-d03810510e47/OceanDNA-b41496.fa --refList OceanDNA-b41496/target_genomes_gtdb.txt --output OceanDNA-b41496/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:10:59,851] [INFO] Task succeeded: fastANI
[2023-03-16 05:10:59,860] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:10:59,860] [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_000420325.1	s__Spongiibacter tropicus	97.9687	1114	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	conclusive
GCF_014705705.1	s__KMU-158 sp014705705	79.5552	218	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016906995.1	s__Spongiibacter marinus	79.4349	388	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	97.69	97.65	0.87	0.86	3	-
GCF_000422345.1	s__Spongiibacter marinus_A	79.3293	395	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272835.1	s__Spongiibacter sp012272835	78.8232	317	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016132545.1	s__CSC3-9 sp016132545	78.1503	253	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__CSC3-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002915595.1	s__Marortus luteolus	77.2117	153	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	-
GCF_017255185.1	s__Parahaliea mediterranea_A	76.6565	107	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447155.2	s__Marinobacter sp001447155	76.4872	70	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061305.1	s__Marinobacterium sp019061305	76.3093	61	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213805.1	s__Pseudomonas_E fulva_B	76.2407	76	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCF_001945445.1	s__Pseudomonas_E sp001945445	76.2407	64	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.91	0.91	2	-
GCF_000378045.1	s__Marinobacterium_A rhizophilum	76.1499	60	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	76.034	64	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_001446935.1	s__Pseudomonas_E sp001446935	75.8748	65	1214	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:10:59,861] [INFO] GTDB search result was written to OceanDNA-b41496/result_gtdb.tsv
[2023-03-16 05:10:59,861] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:10:59,863] [INFO] DFAST_QC result json was written to OceanDNA-b41496/dqc_result.json
[2023-03-16 05:10:59,863] [INFO] DFAST_QC completed!
[2023-03-16 05:10:59,863] [INFO] Total running time: 0h1m49s