[2023-03-15 16:14:47,334] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:14:47,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:14:47,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg879a9629-3379-46c2-afac-72a79751de6b/dqc_reference
[2023-03-15 16:14:49,237] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:14:49,239] [INFO] Task started: Prodigal
[2023-03-15 16:14:49,239] [INFO] Running command: cat /var/lib/cwl/stgc1969bfe-c580-4c46-a444-5149bef10019/OceanDNA-b30146.fa | prodigal -d OceanDNA-b30146/cds.fna -a OceanDNA-b30146/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:15:14,750] [INFO] Task succeeded: Prodigal
[2023-03-15 16:15:14,750] [INFO] Task started: HMMsearch
[2023-03-15 16:15:14,750] [INFO] Running command: hmmsearch --tblout OceanDNA-b30146/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg879a9629-3379-46c2-afac-72a79751de6b/dqc_reference/reference_markers.hmm OceanDNA-b30146/protein.faa > /dev/null
[2023-03-15 16:15:14,982] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:15:14,983] [INFO] Found 6/6 markers.
[2023-03-15 16:15:15,021] [INFO] Query marker FASTA was written to OceanDNA-b30146/markers.fasta
[2023-03-15 16:15:15,022] [INFO] Task started: Blastn
[2023-03-15 16:15:15,022] [INFO] Running command: blastn -query OceanDNA-b30146/markers.fasta -db /var/lib/cwl/stg879a9629-3379-46c2-afac-72a79751de6b/dqc_reference/reference_markers.fasta -out OceanDNA-b30146/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:15,992] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:16,000] [INFO] Selected 15 target genomes.
[2023-03-15 16:15:16,000] [INFO] Target genome list was writen to OceanDNA-b30146/target_genomes.txt
[2023-03-15 16:15:16,009] [INFO] Task started: fastANI
[2023-03-15 16:15:16,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1969bfe-c580-4c46-a444-5149bef10019/OceanDNA-b30146.fa --refList OceanDNA-b30146/target_genomes.txt --output OceanDNA-b30146/fastani_result.tsv --threads 1
[2023-03-15 16:15:29,835] [INFO] Task succeeded: fastANI
[2023-03-15 16:15:29,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg879a9629-3379-46c2-afac-72a79751de6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:15:29,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg879a9629-3379-46c2-afac-72a79751de6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:15:29,845] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 16:15:29,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 16:15:29,845] [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
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	98.3093	1308	1349	95	conclusive
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	80.7817	836	1349	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	80.7619	831	1349	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	80.3691	761	1349	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	80.3533	779	1349	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.9342	729	1349	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.927	702	1349	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	79.8839	654	1349	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	79.8461	664	1349	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.594	641	1349	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.2778	496	1349	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.2323	500	1349	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9931	405	1349	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.8645	396	1349	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8853	280	1349	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:15:29,847] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30146/tc_result.tsv
[2023-03-15 16:15:29,847] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:15:29,847] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:15:29,847] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg879a9629-3379-46c2-afac-72a79751de6b/dqc_reference/checkm_data
[2023-03-15 16:15:29,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:15:29,859] [INFO] Task started: CheckM
[2023-03-15 16:15:29,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30146/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30146/checkm_input OceanDNA-b30146/checkm_result
[2023-03-15 16:17:01,762] [INFO] Task succeeded: CheckM
[2023-03-15 16:17:01,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:17:01,766] [INFO] ===== Completeness check finished =====
[2023-03-15 16:17:01,766] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:17:01,767] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30146/markers.fasta)
[2023-03-15 16:17:01,768] [INFO] Task started: Blastn
[2023-03-15 16:17:01,768] [INFO] Running command: blastn -query OceanDNA-b30146/markers.fasta -db /var/lib/cwl/stg879a9629-3379-46c2-afac-72a79751de6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30146/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:17:03,780] [INFO] Task succeeded: Blastn
[2023-03-15 16:17:03,781] [INFO] Selected 12 target genomes.
[2023-03-15 16:17:03,781] [INFO] Target genome list was writen to OceanDNA-b30146/target_genomes_gtdb.txt
[2023-03-15 16:17:03,831] [INFO] Task started: fastANI
[2023-03-15 16:17:03,831] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1969bfe-c580-4c46-a444-5149bef10019/OceanDNA-b30146.fa --refList OceanDNA-b30146/target_genomes_gtdb.txt --output OceanDNA-b30146/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:17:17,930] [INFO] Task succeeded: fastANI
[2023-03-15 16:17:17,938] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:17:17,938] [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_900100085.1	s__Salipiger marinus	98.2911	1309	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	conclusive
GCF_001687105.1	s__Salipiger sp001687105	81.4029	847	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_001975705.1	s__Salipiger abyssi	81.2121	776	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	81.1766	750	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223355.1	s__Salipiger pacificus_B	80.9083	824	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	80.8943	591	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	80.8274	789	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_900116195.1	s__Salipiger pacificus	80.7996	826	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900102075.1	s__Salipiger thiooxidans	80.3872	759	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_000153725.1	s__Salipiger bermudensis	80.3611	779	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_000442255.1	s__Salipiger mucosus	79.9631	734	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	79.9275	729	1349	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
--------------------------------------------------------------------------------
[2023-03-15 16:17:17,938] [INFO] GTDB search result was written to OceanDNA-b30146/result_gtdb.tsv
[2023-03-15 16:17:17,938] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:17:17,940] [INFO] DFAST_QC result json was written to OceanDNA-b30146/dqc_result.json
[2023-03-15 16:17:17,940] [INFO] DFAST_QC completed!
[2023-03-15 16:17:17,940] [INFO] Total running time: 0h2m31s