[2023-03-15 23:07:02,632] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,633] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg54fd93be-0aff-40d7-a500-d0752ec7803c/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,967] [INFO] Running command: cat /var/lib/cwl/stgfba46f6e-7489-4c81-adf6-05d78bc312e4/OceanDNA-b24879.fa | prodigal -d OceanDNA-b24879/cds.fna -a OceanDNA-b24879/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:22,668] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:22,669] [INFO] Task started: HMMsearch
[2023-03-15 23:07:22,669] [INFO] Running command: hmmsearch --tblout OceanDNA-b24879/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54fd93be-0aff-40d7-a500-d0752ec7803c/dqc_reference/reference_markers.hmm OceanDNA-b24879/protein.faa > /dev/null
[2023-03-15 23:07:22,895] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:22,895] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfba46f6e-7489-4c81-adf6-05d78bc312e4/OceanDNA-b24879.fa]
[2023-03-15 23:07:22,937] [INFO] Query marker FASTA was written to OceanDNA-b24879/markers.fasta
[2023-03-15 23:07:22,939] [INFO] Task started: Blastn
[2023-03-15 23:07:22,939] [INFO] Running command: blastn -query OceanDNA-b24879/markers.fasta -db /var/lib/cwl/stg54fd93be-0aff-40d7-a500-d0752ec7803c/dqc_reference/reference_markers.fasta -out OceanDNA-b24879/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:23,655] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:23,656] [INFO] Selected 25 target genomes.
[2023-03-15 23:07:23,656] [INFO] Target genome list was writen to OceanDNA-b24879/target_genomes.txt
[2023-03-15 23:07:23,694] [INFO] Task started: fastANI
[2023-03-15 23:07:23,694] [INFO] Running command: fastANI --query /var/lib/cwl/stgfba46f6e-7489-4c81-adf6-05d78bc312e4/OceanDNA-b24879.fa --refList OceanDNA-b24879/target_genomes.txt --output OceanDNA-b24879/fastani_result.tsv --threads 1
[2023-03-15 23:07:39,677] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:39,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54fd93be-0aff-40d7-a500-d0752ec7803c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:39,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54fd93be-0aff-40d7-a500-d0752ec7803c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:39,687] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:39,688] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:07:39,688] [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
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	77.665	362	969	95	below_threshold
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	77.487	278	969	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	77.077	248	969	95	below_threshold
Tepidicaulis marinus	strain=MA2	GCA_000739695.1	1333998	1333998	type	True	76.4944	164	969	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	75.8499	51	969	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.8206	61	969	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	75.7278	63	969	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	75.6141	60	969	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_016584015.1	1080	1080	type	True	75.5429	51	969	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_900102695.1	1080	1080	type	True	75.5201	52	969	95	below_threshold
Afifella marina	strain=DSM 2698	GCA_003258905.1	1080	1080	type	True	75.5201	52	969	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	75.4255	60	969	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	75.4171	57	969	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	75.4035	51	969	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_019684215.1	1138189	1138189	type	True	75.3649	54	969	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_017357245.1	1138189	1138189	type	True	75.3649	54	969	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:07:39,688] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24879/tc_result.tsv
[2023-03-15 23:07:39,688] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:39,688] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:39,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54fd93be-0aff-40d7-a500-d0752ec7803c/dqc_reference/checkm_data
[2023-03-15 23:07:39,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:39,694] [INFO] Task started: CheckM
[2023-03-15 23:07:39,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24879/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24879/checkm_input OceanDNA-b24879/checkm_result
[2023-03-15 23:08:28,358] [INFO] Task succeeded: CheckM
[2023-03-15 23:08:28,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:08:28,470] [INFO] ===== Completeness check finished =====
[2023-03-15 23:08:28,470] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:08:28,471] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24879/markers.fasta)
[2023-03-15 23:08:28,472] [INFO] Task started: Blastn
[2023-03-15 23:08:28,472] [INFO] Running command: blastn -query OceanDNA-b24879/markers.fasta -db /var/lib/cwl/stg54fd93be-0aff-40d7-a500-d0752ec7803c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24879/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:08:29,754] [INFO] Task succeeded: Blastn
[2023-03-15 23:08:29,755] [INFO] Selected 16 target genomes.
[2023-03-15 23:08:29,755] [INFO] Target genome list was writen to OceanDNA-b24879/target_genomes_gtdb.txt
[2023-03-15 23:08:29,815] [INFO] Task started: fastANI
[2023-03-15 23:08:29,815] [INFO] Running command: fastANI --query /var/lib/cwl/stgfba46f6e-7489-4c81-adf6-05d78bc312e4/OceanDNA-b24879.fa --refList OceanDNA-b24879/target_genomes_gtdb.txt --output OceanDNA-b24879/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:08:40,789] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:40,798] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:08:40,798] [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_009184905.1	s__Parvibaculum sedimenti	77.665	362	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889655.1	s__Parvibaculum sp903889655	77.6619	361	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.81	99.81	0.91	0.91	2	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	77.487	278	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841195.1	s__Parvibaculum sp002841195	77.3866	259	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124805.1	s__Parvibaculum sp016124805	77.1516	246	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	77.077	248	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480495.1	s__Parvibaculum sp002480495	77.0018	248	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.50	98.87	0.94	0.88	9	-
GCA_014359855.1	s__Parvibaculum sp014359855	76.9459	161	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842875.1	s__Parvibaculum sp002842875	76.875	242	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	76.8406	247	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCA_013823365.1	s__Parvibaculum sp013823365	76.739	209	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102695.1	s__Afifella marina	75.5201	52	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Afifella	95.0	99.99	99.99	1.00	0.99	5	-
GCF_003432385.1	s__Breoghania sp003432385	75.3227	67	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Breoghania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993735.1	s__Chelativorans alearense	75.1058	50	969	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:08:40,800] [INFO] GTDB search result was written to OceanDNA-b24879/result_gtdb.tsv
[2023-03-15 23:08:40,805] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:08:40,811] [INFO] DFAST_QC result json was written to OceanDNA-b24879/dqc_result.json
[2023-03-15 23:08:40,811] [INFO] DFAST_QC completed!
[2023-03-15 23:08:40,811] [INFO] Total running time: 0h1m38s