[2023-03-15 13:20:51,548] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,548] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,548] [INFO] DQC Reference Directory: /var/lib/cwl/stge82af9e9-4855-4fbd-96b9-f1dc562491df/dqc_reference
[2023-03-15 13:20:52,638] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,639] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,639] [INFO] Running command: cat /var/lib/cwl/stg9a303e54-38e3-4d09-8095-678413a54246/OceanDNA-b11455.fa | prodigal -d OceanDNA-b11455/cds.fna -a OceanDNA-b11455/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:17,395] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:17,395] [INFO] Task started: HMMsearch
[2023-03-15 13:21:17,395] [INFO] Running command: hmmsearch --tblout OceanDNA-b11455/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge82af9e9-4855-4fbd-96b9-f1dc562491df/dqc_reference/reference_markers.hmm OceanDNA-b11455/protein.faa > /dev/null
[2023-03-15 13:21:17,684] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:17,685] [INFO] Found 6/6 markers.
[2023-03-15 13:21:17,709] [INFO] Query marker FASTA was written to OceanDNA-b11455/markers.fasta
[2023-03-15 13:21:17,710] [INFO] Task started: Blastn
[2023-03-15 13:21:17,710] [INFO] Running command: blastn -query OceanDNA-b11455/markers.fasta -db /var/lib/cwl/stge82af9e9-4855-4fbd-96b9-f1dc562491df/dqc_reference/reference_markers.fasta -out OceanDNA-b11455/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:18,310] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:18,311] [INFO] Selected 18 target genomes.
[2023-03-15 13:21:18,312] [INFO] Target genome list was writen to OceanDNA-b11455/target_genomes.txt
[2023-03-15 13:21:18,324] [INFO] Task started: fastANI
[2023-03-15 13:21:18,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a303e54-38e3-4d09-8095-678413a54246/OceanDNA-b11455.fa --refList OceanDNA-b11455/target_genomes.txt --output OceanDNA-b11455/fastani_result.tsv --threads 1
[2023-03-15 13:21:32,502] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:32,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge82af9e9-4855-4fbd-96b9-f1dc562491df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:32,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge82af9e9-4855-4fbd-96b9-f1dc562491df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:32,513] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 13:21:32,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 13:21:32,513] [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
Zunongwangia profunda	strain=SMA-87	GCA_000023465.1	398743	398743	type	True	99.3149	1280	1303	95	conclusive
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	83.7514	939	1303	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	83.3223	879	1303	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	79.3424	171	1303	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.8247	231	1303	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	77.3815	214	1303	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	77.1575	219	1303	95	below_threshold
Salegentibacter maritimus	strain=F63223	GCA_016236915.1	2794347	2794347	type	True	77.0426	210	1303	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	76.9668	144	1303	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	76.7833	155	1303	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	76.7614	155	1303	95	below_threshold
Salegentibacter echinorum	strain=DSM 24579	GCA_900129445.1	1073325	1073325	type	True	76.6883	191	1303	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.3922	61	1303	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	75.9241	80	1303	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.8469	59	1303	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	75.794	69	1303	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:32,514] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11455/tc_result.tsv
[2023-03-15 13:21:32,514] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:32,514] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:32,514] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge82af9e9-4855-4fbd-96b9-f1dc562491df/dqc_reference/checkm_data
[2023-03-15 13:21:32,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:32,521] [INFO] Task started: CheckM
[2023-03-15 13:21:32,521] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11455/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11455/checkm_input OceanDNA-b11455/checkm_result
[2023-03-15 13:22:33,774] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:33,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.27%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:33,778] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:33,778] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:33,778] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11455/markers.fasta)
[2023-03-15 13:22:33,779] [INFO] Task started: Blastn
[2023-03-15 13:22:33,779] [INFO] Running command: blastn -query OceanDNA-b11455/markers.fasta -db /var/lib/cwl/stge82af9e9-4855-4fbd-96b9-f1dc562491df/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11455/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:34,615] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:34,616] [INFO] Selected 15 target genomes.
[2023-03-15 13:22:34,616] [INFO] Target genome list was writen to OceanDNA-b11455/target_genomes_gtdb.txt
[2023-03-15 13:22:34,634] [INFO] Task started: fastANI
[2023-03-15 13:22:34,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a303e54-38e3-4d09-8095-678413a54246/OceanDNA-b11455.fa --refList OceanDNA-b11455/target_genomes_gtdb.txt --output OceanDNA-b11455/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:44,402] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:44,410] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:22:44,410] [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_000023465.1	s__Zunongwangia profunda	99.3149	1280	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	99.17	98.44	0.93	0.80	11	conclusive
GCF_002094855.1	s__Zunongwangia atlantica	83.7807	936	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112105.1	s__Zunongwangia mangrovi	83.3322	878	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499555.1	s__Mesonia oceanica	79.315	172	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCF_002900095.1	s__Salegentibacter mishustinae	78.1211	249	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_900168265.1	s__Salegentibacter salarius	77.214	217	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_900113135.1	s__Salegentibacter agarivorans	77.1078	262	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_016236915.1	s__Salegentibacter maritimus	77.042	210	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
GCF_000423405.1	s__Mesonia mobilis	76.7614	155	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900129445.1	s__Salegentibacter echinorum	76.6994	190	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964435.1	s__Mesonia sp012964435	76.5572	151	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900104765.1	s__Gillisia sp900104765	76.4689	131	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_011762485.1	s__Yeosuana marina	75.794	69	1303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:44,411] [INFO] GTDB search result was written to OceanDNA-b11455/result_gtdb.tsv
[2023-03-15 13:22:44,411] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:44,414] [INFO] DFAST_QC result json was written to OceanDNA-b11455/dqc_result.json
[2023-03-15 13:22:44,414] [INFO] DFAST_QC completed!
[2023-03-15 13:22:44,414] [INFO] Total running time: 0h1m53s