[2023-03-18 00:53:42,512] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,512] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg0511ed30-01d9-48d9-b790-59cbbbb6f669/dqc_reference
[2023-03-18 00:53:43,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:43,616] [INFO] Task started: Prodigal
[2023-03-18 00:53:43,616] [INFO] Running command: cat /var/lib/cwl/stg53301a0c-3d90-4278-b64e-9517d7478f12/OceanDNA-b29930.fa | prodigal -d OceanDNA-b29930/cds.fna -a OceanDNA-b29930/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:58,548] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:58,549] [INFO] Task started: HMMsearch
[2023-03-18 00:53:58,549] [INFO] Running command: hmmsearch --tblout OceanDNA-b29930/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0511ed30-01d9-48d9-b790-59cbbbb6f669/dqc_reference/reference_markers.hmm OceanDNA-b29930/protein.faa > /dev/null
[2023-03-18 00:53:58,742] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:58,742] [INFO] Found 6/6 markers.
[2023-03-18 00:53:58,762] [INFO] Query marker FASTA was written to OceanDNA-b29930/markers.fasta
[2023-03-18 00:53:58,763] [INFO] Task started: Blastn
[2023-03-18 00:53:58,763] [INFO] Running command: blastn -query OceanDNA-b29930/markers.fasta -db /var/lib/cwl/stg0511ed30-01d9-48d9-b790-59cbbbb6f669/dqc_reference/reference_markers.fasta -out OceanDNA-b29930/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:59,397] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:59,398] [INFO] Selected 30 target genomes.
[2023-03-18 00:53:59,399] [INFO] Target genome list was writen to OceanDNA-b29930/target_genomes.txt
[2023-03-18 00:53:59,417] [INFO] Task started: fastANI
[2023-03-18 00:53:59,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg53301a0c-3d90-4278-b64e-9517d7478f12/OceanDNA-b29930.fa --refList OceanDNA-b29930/target_genomes.txt --output OceanDNA-b29930/fastani_result.tsv --threads 1
[2023-03-18 00:54:17,602] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:17,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0511ed30-01d9-48d9-b790-59cbbbb6f669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:17,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0511ed30-01d9-48d9-b790-59cbbbb6f669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:17,614] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 00:54:17,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 00:54:17,615] [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
Planktomarina temperata	strain=RCA23	GCA_000738435.1	1284658	1284658	type	True	98.9249	732	751	95	conclusive
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.2596	72	751	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	76.0912	65	751	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	76.029	62	751	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.029	62	751	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	76.0219	68	751	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	75.9847	60	751	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	75.865	71	751	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	75.823	59	751	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	75.8005	54	751	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_002796795.1	1156985	1156985	type	True	75.798	63	751	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_900102795.1	1156985	1156985	type	True	75.7979	63	751	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	75.7431	66	751	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	75.7164	82	751	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	75.7071	61	751	95	below_threshold
Roseovarius bejariae	strain=A21	GCA_009669325.1	2576383	2576383	type	True	75.6593	59	751	95	below_threshold
Oceaniglobus ichthyenteri	strain=YLY08	GCA_003057885.1	2136177	2136177	type	True	75.6526	73	751	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	75.5504	64	751	95	below_threshold
Pseudorhodobacter turbinis	strain=S12M18	GCA_005234135.1	2500533	2500533	type	True	75.4486	69	751	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	75.3606	62	751	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:17,615] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29930/tc_result.tsv
[2023-03-18 00:54:17,615] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:17,615] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:17,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0511ed30-01d9-48d9-b790-59cbbbb6f669/dqc_reference/checkm_data
[2023-03-18 00:54:17,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:17,630] [INFO] Task started: CheckM
[2023-03-18 00:54:17,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29930/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29930/checkm_input OceanDNA-b29930/checkm_result
[2023-03-18 00:54:57,993] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:57,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:54:58,024] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:58,024] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:58,024] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29930/markers.fasta)
[2023-03-18 00:54:58,025] [INFO] Task started: Blastn
[2023-03-18 00:54:58,026] [INFO] Running command: blastn -query OceanDNA-b29930/markers.fasta -db /var/lib/cwl/stg0511ed30-01d9-48d9-b790-59cbbbb6f669/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29930/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:59,117] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:59,124] [INFO] Selected 9 target genomes.
[2023-03-18 00:54:59,124] [INFO] Target genome list was writen to OceanDNA-b29930/target_genomes_gtdb.txt
[2023-03-18 00:54:59,156] [INFO] Task started: fastANI
[2023-03-18 00:54:59,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg53301a0c-3d90-4278-b64e-9517d7478f12/OceanDNA-b29930.fa --refList OceanDNA-b29930/target_genomes_gtdb.txt --output OceanDNA-b29930/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:55:04,391] [INFO] Task succeeded: fastANI
[2023-03-18 00:55:04,396] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:55:04,397] [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_000738435.1	s__Planktomarina temperata	98.9249	732	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.99	97.76	0.97	0.80	20	conclusive
GCA_016780825.1	s__Planktomarina sp016780825	90.4885	617	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181815.1	s__Planktomarina sp905181815	89.8121	647	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683685.1	s__Planktomarina sp002683685	87.089	483	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	95.59	95.45	0.70	0.67	6	-
GCA_905182455.1	s__Planktomarina sp905182455	78.1594	280	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981705.1	s__Planktomarina sp000981705	77.4816	160	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.80	98.80	0.86	0.86	2	-
GCF_001458175.1	s__Shimia marina	76.026	62	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_000203975.2	s__Leisingera sp000203975	75.9625	60	751	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
--------------------------------------------------------------------------------
[2023-03-18 00:55:04,397] [INFO] GTDB search result was written to OceanDNA-b29930/result_gtdb.tsv
[2023-03-18 00:55:04,397] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:55:04,399] [INFO] DFAST_QC result json was written to OceanDNA-b29930/dqc_result.json
[2023-03-18 00:55:04,399] [INFO] DFAST_QC completed!
[2023-03-18 00:55:04,399] [INFO] Total running time: 0h1m22s