[2023-03-15 13:20:51,590] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,590] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg15000b55-473a-43a3-a69c-defccdc7c68b/dqc_reference
[2023-03-15 13:20:52,716] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,716] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,717] [INFO] Running command: cat /var/lib/cwl/stg136b224c-67f8-4fa6-957d-f1ef61287d51/OceanDNA-b33280.fa | prodigal -d OceanDNA-b33280/cds.fna -a OceanDNA-b33280/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:06,864] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:06,864] [INFO] Task started: HMMsearch
[2023-03-15 13:21:06,864] [INFO] Running command: hmmsearch --tblout OceanDNA-b33280/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15000b55-473a-43a3-a69c-defccdc7c68b/dqc_reference/reference_markers.hmm OceanDNA-b33280/protein.faa > /dev/null
[2023-03-15 13:21:07,120] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:07,120] [INFO] Found 6/6 markers.
[2023-03-15 13:21:07,138] [INFO] Query marker FASTA was written to OceanDNA-b33280/markers.fasta
[2023-03-15 13:21:07,138] [INFO] Task started: Blastn
[2023-03-15 13:21:07,138] [INFO] Running command: blastn -query OceanDNA-b33280/markers.fasta -db /var/lib/cwl/stg15000b55-473a-43a3-a69c-defccdc7c68b/dqc_reference/reference_markers.fasta -out OceanDNA-b33280/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:07,953] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:07,954] [INFO] Selected 27 target genomes.
[2023-03-15 13:21:07,954] [INFO] Target genome list was writen to OceanDNA-b33280/target_genomes.txt
[2023-03-15 13:21:07,973] [INFO] Task started: fastANI
[2023-03-15 13:21:07,973] [INFO] Running command: fastANI --query /var/lib/cwl/stg136b224c-67f8-4fa6-957d-f1ef61287d51/OceanDNA-b33280.fa --refList OceanDNA-b33280/target_genomes.txt --output OceanDNA-b33280/fastani_result.tsv --threads 1
[2023-03-15 13:21:29,845] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:29,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15000b55-473a-43a3-a69c-defccdc7c68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:29,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15000b55-473a-43a3-a69c-defccdc7c68b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:29,861] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:29,861] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:29,861] [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
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.0437	314	699	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.0045	279	699	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.9629	289	699	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	78.9578	316	699	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	78.7729	267	699	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	78.7586	321	699	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	78.7252	276	699	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	78.6963	277	699	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	78.6499	275	699	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	78.438	243	699	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	78.4108	237	699	95	below_threshold
Inhella proteolytica	strain=1Y17	GCA_016093275.1	2795029	2795029	type	True	78.3856	255	699	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	78.3232	250	699	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	78.3213	233	699	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.2799	278	699	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	78.2746	266	699	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	78.2369	294	699	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.1987	250	699	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	78.1133	235	699	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	77.9603	251	699	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	77.9318	221	699	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	77.8858	247	699	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	77.7872	236	699	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	77.6035	233	699	95	below_threshold
Tepidimonas taiwanensis	strain=I1-1	GCA_007556675.1	307486	307486	type	True	77.5349	179	699	95	below_threshold
Tepidimonas taiwanensis	strain=LMG 22826	GCA_020162115.1	307486	307486	type	True	77.5297	183	699	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	77.3244	127	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:29,861] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33280/tc_result.tsv
[2023-03-15 13:21:29,862] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:29,862] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:29,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15000b55-473a-43a3-a69c-defccdc7c68b/dqc_reference/checkm_data
[2023-03-15 13:21:29,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:29,867] [INFO] Task started: CheckM
[2023-03-15 13:21:29,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33280/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33280/checkm_input OceanDNA-b33280/checkm_result
[2023-03-15 13:22:16,177] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:16,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.79%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:16,180] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:16,180] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:16,180] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33280/markers.fasta)
[2023-03-15 13:22:16,181] [INFO] Task started: Blastn
[2023-03-15 13:22:16,181] [INFO] Running command: blastn -query OceanDNA-b33280/markers.fasta -db /var/lib/cwl/stg15000b55-473a-43a3-a69c-defccdc7c68b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33280/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:17,735] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:17,736] [INFO] Selected 17 target genomes.
[2023-03-15 13:22:17,736] [INFO] Target genome list was writen to OceanDNA-b33280/target_genomes_gtdb.txt
[2023-03-15 13:22:17,753] [INFO] Task started: fastANI
[2023-03-15 13:22:17,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg136b224c-67f8-4fa6-957d-f1ef61287d51/OceanDNA-b33280.fa --refList OceanDNA-b33280/target_genomes_gtdb.txt --output OceanDNA-b33280/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:31,667] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:31,677] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:22:31,678] [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
GCA_009923315.1	s__RFTU01 sp009923315	99.4943	631	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	99.55	99.38	0.93	0.92	4	conclusive
GCA_009925955.1	s__RFTU01 sp009925955	82.3839	253	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009918225.1	s__RFTU01 sp009918225	81.7744	350	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	98.76	98.76	0.88	0.88	2	-
GCA_016868355.1	s__RFTU01 sp016868355	80.8588	469	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430725.1	s__Azohydromonas australica	79.0296	315	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571085.1	s__Azohydromonas lata	78.9541	290	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000244995.1	s__Aquabacterium_A sp000244995	78.9366	329	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	78.9307	318	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828235.1	s__Rubrivivax sp903828235	78.8308	333	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.94	99.91	0.96	0.96	5	-
GCA_003265685.1	s__Piscinibacter caeni	78.5618	305	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219375.1	s__Aquabacterium sp016219375	78.5549	258	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938815.1	s__Rubrivivax sp903938815	78.5411	300	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.66	99.41	0.96	0.94	10	-
GCF_014174515.1	s__WAJ17 sp014174515	78.4577	271	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WAJ17	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205845.1	s__Pelomonas puraquae	78.2369	294	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pelomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790225.1	s__Rubrivivax sp016790225	78.13	288	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503085.1	s__Paucibacter_A sp005503085	78.0059	280	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009906855.1	s__Xylophilus rhododendri	77.6035	233	699	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xylophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:31,678] [INFO] GTDB search result was written to OceanDNA-b33280/result_gtdb.tsv
[2023-03-15 13:22:31,678] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:31,681] [INFO] DFAST_QC result json was written to OceanDNA-b33280/dqc_result.json
[2023-03-15 13:22:31,681] [INFO] DFAST_QC completed!
[2023-03-15 13:22:31,681] [INFO] Total running time: 0h1m40s