[2023-03-17 09:33:09,732] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:33:09,732] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:33:09,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg0497fac7-0d07-47ad-8156-6903e3637303/dqc_reference
[2023-03-17 09:33:10,857] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:33:10,857] [INFO] Task started: Prodigal
[2023-03-17 09:33:10,857] [INFO] Running command: cat /var/lib/cwl/stgfec667f1-04b1-49f3-b965-01856c6c8391/OceanDNA-b30138.fa | prodigal -d OceanDNA-b30138/cds.fna -a OceanDNA-b30138/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:33:41,474] [INFO] Task succeeded: Prodigal
[2023-03-17 09:33:41,475] [INFO] Task started: HMMsearch
[2023-03-17 09:33:41,475] [INFO] Running command: hmmsearch --tblout OceanDNA-b30138/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0497fac7-0d07-47ad-8156-6903e3637303/dqc_reference/reference_markers.hmm OceanDNA-b30138/protein.faa > /dev/null
[2023-03-17 09:33:41,701] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:33:41,702] [INFO] Found 6/6 markers.
[2023-03-17 09:33:41,730] [INFO] Query marker FASTA was written to OceanDNA-b30138/markers.fasta
[2023-03-17 09:33:41,731] [INFO] Task started: Blastn
[2023-03-17 09:33:41,731] [INFO] Running command: blastn -query OceanDNA-b30138/markers.fasta -db /var/lib/cwl/stg0497fac7-0d07-47ad-8156-6903e3637303/dqc_reference/reference_markers.fasta -out OceanDNA-b30138/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:33:42,628] [INFO] Task succeeded: Blastn
[2023-03-17 09:33:42,629] [INFO] Selected 21 target genomes.
[2023-03-17 09:33:42,630] [INFO] Target genome list was writen to OceanDNA-b30138/target_genomes.txt
[2023-03-17 09:33:43,273] [INFO] Task started: fastANI
[2023-03-17 09:33:43,274] [INFO] Running command: fastANI --query /var/lib/cwl/stgfec667f1-04b1-49f3-b965-01856c6c8391/OceanDNA-b30138.fa --refList OceanDNA-b30138/target_genomes.txt --output OceanDNA-b30138/fastani_result.tsv --threads 1
[2023-03-17 09:34:03,144] [INFO] Task succeeded: fastANI
[2023-03-17 09:34:03,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0497fac7-0d07-47ad-8156-6903e3637303/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:34:03,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0497fac7-0d07-47ad-8156-6903e3637303/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:34:03,156] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:34:03,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:34:03,157] [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
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	80.2035	852	1548	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	80.1262	855	1548	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	80.0749	774	1548	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.8761	714	1548	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.8364	738	1548	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.7012	723	1548	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.4148	746	1548	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	79.388	752	1548	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	79.2853	664	1548	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	79.1755	563	1548	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.1617	651	1548	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	79.0687	693	1548	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	79.063	600	1548	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	79.0629	599	1548	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	79.0011	603	1548	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.9994	571	1548	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	78.8873	516	1548	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.6136	673	1548	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	78.6129	519	1548	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.9664	435	1548	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.3651	298	1548	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:34:03,157] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30138/tc_result.tsv
[2023-03-17 09:34:03,157] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:34:03,157] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:34:03,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0497fac7-0d07-47ad-8156-6903e3637303/dqc_reference/checkm_data
[2023-03-17 09:34:03,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:34:03,174] [INFO] Task started: CheckM
[2023-03-17 09:34:03,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30138/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30138/checkm_input OceanDNA-b30138/checkm_result
[2023-03-17 09:35:21,357] [INFO] Task succeeded: CheckM
[2023-03-17 09:35:21,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:35:21,360] [INFO] ===== Completeness check finished =====
[2023-03-17 09:35:21,360] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:35:21,361] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30138/markers.fasta)
[2023-03-17 09:35:21,362] [INFO] Task started: Blastn
[2023-03-17 09:35:21,362] [INFO] Running command: blastn -query OceanDNA-b30138/markers.fasta -db /var/lib/cwl/stg0497fac7-0d07-47ad-8156-6903e3637303/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30138/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:35:22,947] [INFO] Task succeeded: Blastn
[2023-03-17 09:35:22,947] [INFO] Selected 15 target genomes.
[2023-03-17 09:35:22,948] [INFO] Target genome list was writen to OceanDNA-b30138/target_genomes_gtdb.txt
[2023-03-17 09:35:23,699] [INFO] Task started: fastANI
[2023-03-17 09:35:23,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgfec667f1-04b1-49f3-b965-01856c6c8391/OceanDNA-b30138.fa --refList OceanDNA-b30138/target_genomes_gtdb.txt --output OceanDNA-b30138/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:35:41,703] [INFO] Task succeeded: fastANI
[2023-03-17 09:35:41,712] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:35:41,712] [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_002814095.1	s__Sagittula sp002814095	99.9691	1537	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000169415.1	s__Sagittula stellata	89.3844	1280	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	81.0189	856	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	80.8766	852	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900184945.1	s__Maliponia aquimaris	80.7388	904	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813235.1	s__Sagittula sp017813235	80.569	918	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	80.3812	826	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	80.1332	854	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900102075.1	s__Salipiger thiooxidans	80.0465	778	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_018224955.1	s__Aestuariicoccus sp018224955	79.8605	767	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	79.6886	634	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196795.1	s__Sagittula marina	79.2998	662	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	79.191	637	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	79.1684	652	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218285.1	s__DP3N28-2 sp019218285	79.0687	693	1548	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DP3N28-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:35:41,713] [INFO] GTDB search result was written to OceanDNA-b30138/result_gtdb.tsv
[2023-03-17 09:35:41,713] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:35:41,715] [INFO] DFAST_QC result json was written to OceanDNA-b30138/dqc_result.json
[2023-03-17 09:35:41,715] [INFO] DFAST_QC completed!
[2023-03-17 09:35:41,715] [INFO] Total running time: 0h2m32s