[2023-03-16 07:55:45,176] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:55:45,177] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:55:45,177] [INFO] DQC Reference Directory: /var/lib/cwl/stgcdade052-9993-43e7-8e8a-84c62fa6a24a/dqc_reference
[2023-03-16 07:55:46,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:55:46,308] [INFO] Task started: Prodigal
[2023-03-16 07:55:46,309] [INFO] Running command: cat /var/lib/cwl/stgc3f8d192-75cd-461d-b324-9fe2d38af089/OceanDNA-b38999.fa | prodigal -d OceanDNA-b38999/cds.fna -a OceanDNA-b38999/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:56:07,710] [INFO] Task succeeded: Prodigal
[2023-03-16 07:56:07,711] [INFO] Task started: HMMsearch
[2023-03-16 07:56:07,711] [INFO] Running command: hmmsearch --tblout OceanDNA-b38999/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcdade052-9993-43e7-8e8a-84c62fa6a24a/dqc_reference/reference_markers.hmm OceanDNA-b38999/protein.faa > /dev/null
[2023-03-16 07:56:07,936] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:56:07,936] [INFO] Found 6/6 markers.
[2023-03-16 07:56:07,958] [INFO] Query marker FASTA was written to OceanDNA-b38999/markers.fasta
[2023-03-16 07:56:07,960] [INFO] Task started: Blastn
[2023-03-16 07:56:07,960] [INFO] Running command: blastn -query OceanDNA-b38999/markers.fasta -db /var/lib/cwl/stgcdade052-9993-43e7-8e8a-84c62fa6a24a/dqc_reference/reference_markers.fasta -out OceanDNA-b38999/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:56:08,607] [INFO] Task succeeded: Blastn
[2023-03-16 07:56:08,607] [INFO] Selected 13 target genomes.
[2023-03-16 07:56:08,608] [INFO] Target genome list was writen to OceanDNA-b38999/target_genomes.txt
[2023-03-16 07:56:08,615] [INFO] Task started: fastANI
[2023-03-16 07:56:08,615] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3f8d192-75cd-461d-b324-9fe2d38af089/OceanDNA-b38999.fa --refList OceanDNA-b38999/target_genomes.txt --output OceanDNA-b38999/fastani_result.tsv --threads 1
[2023-03-16 07:56:19,261] [INFO] Task succeeded: fastANI
[2023-03-16 07:56:19,262] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcdade052-9993-43e7-8e8a-84c62fa6a24a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:56:19,262] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcdade052-9993-43e7-8e8a-84c62fa6a24a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:56:19,270] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2023-03-16 07:56:19,270] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-16 07:56:19,270] [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
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	97.7288	1078	1152	95	inconclusive
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	97.6982	1080	1152	95	inconclusive
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	96.4351	1046	1152	95	inconclusive
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	88.2497	1008	1152	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	82.4977	852	1152	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	82.4588	828	1152	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	81.6828	769	1152	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.1199	488	1152	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	80.1145	581	1152	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	79.5295	560	1152	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.2442	533	1152	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.2676	398	1152	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:56:19,270] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38999/tc_result.tsv
[2023-03-16 07:56:19,270] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:56:19,270] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:56:19,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcdade052-9993-43e7-8e8a-84c62fa6a24a/dqc_reference/checkm_data
[2023-03-16 07:56:19,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:56:19,343] [INFO] Task started: CheckM
[2023-03-16 07:56:19,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38999/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38999/checkm_input OceanDNA-b38999/checkm_result
[2023-03-16 07:57:13,329] [INFO] Task succeeded: CheckM
[2023-03-16 07:57:13,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:57:13,335] [INFO] ===== Completeness check finished =====
[2023-03-16 07:57:13,335] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:57:13,336] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38999/markers.fasta)
[2023-03-16 07:57:13,336] [INFO] Task started: Blastn
[2023-03-16 07:57:13,337] [INFO] Running command: blastn -query OceanDNA-b38999/markers.fasta -db /var/lib/cwl/stgcdade052-9993-43e7-8e8a-84c62fa6a24a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38999/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:57:14,448] [INFO] Task succeeded: Blastn
[2023-03-16 07:57:14,452] [INFO] Selected 9 target genomes.
[2023-03-16 07:57:14,452] [INFO] Target genome list was writen to OceanDNA-b38999/target_genomes_gtdb.txt
[2023-03-16 07:57:14,589] [INFO] Task started: fastANI
[2023-03-16 07:57:14,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3f8d192-75cd-461d-b324-9fe2d38af089/OceanDNA-b38999.fa --refList OceanDNA-b38999/target_genomes_gtdb.txt --output OceanDNA-b38999/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:57:22,722] [INFO] Task succeeded: fastANI
[2023-03-16 07:57:22,728] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 07:57:22,728] [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_002933295.1	s__Marinobacter flavimaris	97.7288	1078	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	inconclusive
GCF_000235625.1	s__Marinobacter manganoxydans_A	96.7318	1049	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	inconclusive
GCF_000166295.1	s__Marinobacter adhaerens	96.4351	1046	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_900188315.1	s__Marinobacter sp900188315	94.9688	991	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.8497	N/A	N/A	N/A	N/A	1	-
GCF_900188435.1	s__Marinobacter sp900188435	89.1166	983	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650915.1	s__Marinobacter sp001650915	89.0932	1023	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCA_003030785.1	s__Marinobacter sp003030785	88.4832	584	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107725.1	s__Marinobacter sp008107725	88.3437	1011	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933275.1	s__Marinobacter maroccanus	88.245	1009	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:57:22,734] [INFO] GTDB search result was written to OceanDNA-b38999/result_gtdb.tsv
[2023-03-16 07:57:22,736] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:57:22,737] [INFO] DFAST_QC result json was written to OceanDNA-b38999/dqc_result.json
[2023-03-16 07:57:22,737] [INFO] DFAST_QC completed!
[2023-03-16 07:57:22,737] [INFO] Total running time: 0h1m38s