[2023-03-15 16:03:33,907] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:03:33,911] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:03:33,911] [INFO] DQC Reference Directory: /var/lib/cwl/stg2efa81dc-46d3-4725-905e-cc125dfa1255/dqc_reference
[2023-03-15 16:03:35,028] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:03:35,029] [INFO] Task started: Prodigal
[2023-03-15 16:03:35,029] [INFO] Running command: cat /var/lib/cwl/stg1d724d41-fc5d-4fcc-9bd1-8916a81e5af2/OceanDNA-b30468.fa | prodigal -d OceanDNA-b30468/cds.fna -a OceanDNA-b30468/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:04:02,855] [INFO] Task succeeded: Prodigal
[2023-03-15 16:04:02,855] [INFO] Task started: HMMsearch
[2023-03-15 16:04:02,855] [INFO] Running command: hmmsearch --tblout OceanDNA-b30468/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2efa81dc-46d3-4725-905e-cc125dfa1255/dqc_reference/reference_markers.hmm OceanDNA-b30468/protein.faa > /dev/null
[2023-03-15 16:04:03,081] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:04:03,082] [INFO] Found 6/6 markers.
[2023-03-15 16:04:03,117] [INFO] Query marker FASTA was written to OceanDNA-b30468/markers.fasta
[2023-03-15 16:04:03,119] [INFO] Task started: Blastn
[2023-03-15 16:04:03,119] [INFO] Running command: blastn -query OceanDNA-b30468/markers.fasta -db /var/lib/cwl/stg2efa81dc-46d3-4725-905e-cc125dfa1255/dqc_reference/reference_markers.fasta -out OceanDNA-b30468/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:04:04,000] [INFO] Task succeeded: Blastn
[2023-03-15 16:04:04,018] [INFO] Selected 24 target genomes.
[2023-03-15 16:04:04,018] [INFO] Target genome list was writen to OceanDNA-b30468/target_genomes.txt
[2023-03-15 16:04:04,032] [INFO] Task started: fastANI
[2023-03-15 16:04:04,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d724d41-fc5d-4fcc-9bd1-8916a81e5af2/OceanDNA-b30468.fa --refList OceanDNA-b30468/target_genomes.txt --output OceanDNA-b30468/fastani_result.tsv --threads 1
[2023-03-15 16:04:22,302] [INFO] Task succeeded: fastANI
[2023-03-15 16:04:22,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2efa81dc-46d3-4725-905e-cc125dfa1255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:04:22,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2efa81dc-46d3-4725-905e-cc125dfa1255/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:04:22,317] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:04:22,317] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:04:22,317] [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
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	93.7089	1258	1412	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	93.7047	1258	1412	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.9361	612	1412	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	78.4676	522	1412	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	78.3529	474	1412	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.2283	513	1412	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.16	435	1412	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	78.1554	447	1412	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.1531	445	1412	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.1317	436	1412	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.9538	512	1412	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.9003	431	1412	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	77.8235	408	1412	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	77.8175	417	1412	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.8045	395	1412	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.7991	398	1412	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.7746	418	1412	95	below_threshold
Shimia sediminis	strain=ZQ172	GCA_003990645.1	2497945	2497945	type	True	77.7694	376	1412	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	77.7234	396	1412	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7052	325	1412	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	77.643	410	1412	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	77.3629	337	1412	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.9105	293	1412	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8812	304	1412	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:04:22,319] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30468/tc_result.tsv
[2023-03-15 16:04:22,323] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:04:22,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:04:22,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2efa81dc-46d3-4725-905e-cc125dfa1255/dqc_reference/checkm_data
[2023-03-15 16:04:22,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:04:22,334] [INFO] Task started: CheckM
[2023-03-15 16:04:22,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30468/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30468/checkm_input OceanDNA-b30468/checkm_result
[2023-03-15 16:05:37,010] [INFO] Task succeeded: CheckM
[2023-03-15 16:05:37,011] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:05:37,058] [INFO] ===== Completeness check finished =====
[2023-03-15 16:05:37,058] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:05:37,059] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30468/markers.fasta)
[2023-03-15 16:05:37,060] [INFO] Task started: Blastn
[2023-03-15 16:05:37,060] [INFO] Running command: blastn -query OceanDNA-b30468/markers.fasta -db /var/lib/cwl/stg2efa81dc-46d3-4725-905e-cc125dfa1255/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30468/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:05:38,791] [INFO] Task succeeded: Blastn
[2023-03-15 16:05:38,795] [INFO] Selected 11 target genomes.
[2023-03-15 16:05:38,795] [INFO] Target genome list was writen to OceanDNA-b30468/target_genomes_gtdb.txt
[2023-03-15 16:05:38,823] [INFO] Task started: fastANI
[2023-03-15 16:05:38,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d724d41-fc5d-4fcc-9bd1-8916a81e5af2/OceanDNA-b30468.fa --refList OceanDNA-b30468/target_genomes_gtdb.txt --output OceanDNA-b30468/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:05:49,326] [INFO] Task succeeded: fastANI
[2023-03-15 16:05:49,333] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:05:49,333] [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_000620505.1	s__Ascidiaceihabitans sp000620505	97.4639	1320	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	93.7089	1258	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	88.8611	1025	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	84.9064	1022	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_003335585.1	s__Sulfitobacter sp003335585	79.9503	723	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	79.6298	661	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.221	514	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854855.1	s__Sulfitobacter sp017854855	78.2071	449	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172095.1	s__Sulfitobacter indolifex	78.1317	436	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.5472	347	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003355.1	s__Donghicola tyrosinivorans	77.3455	339	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Donghicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:05:49,339] [INFO] GTDB search result was written to OceanDNA-b30468/result_gtdb.tsv
[2023-03-15 16:05:49,351] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:05:49,358] [INFO] DFAST_QC result json was written to OceanDNA-b30468/dqc_result.json
[2023-03-15 16:05:49,358] [INFO] DFAST_QC completed!
[2023-03-15 16:05:49,358] [INFO] Total running time: 0h2m15s