[2023-03-17 02:03:51,355] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:03:51,356] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:03:51,356] [INFO] DQC Reference Directory: /var/lib/cwl/stg445760c5-303e-48c1-a8a8-a69c1565266f/dqc_reference
[2023-03-17 02:03:52,466] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:03:52,466] [INFO] Task started: Prodigal
[2023-03-17 02:03:52,467] [INFO] Running command: cat /var/lib/cwl/stg40037c56-825e-4d36-ac44-6c640005326a/OceanDNA-b30134.fa | prodigal -d OceanDNA-b30134/cds.fna -a OceanDNA-b30134/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:04:10,039] [INFO] Task succeeded: Prodigal
[2023-03-17 02:04:10,040] [INFO] Task started: HMMsearch
[2023-03-17 02:04:10,040] [INFO] Running command: hmmsearch --tblout OceanDNA-b30134/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg445760c5-303e-48c1-a8a8-a69c1565266f/dqc_reference/reference_markers.hmm OceanDNA-b30134/protein.faa > /dev/null
[2023-03-17 02:04:10,241] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:04:10,241] [INFO] Found 6/6 markers.
[2023-03-17 02:04:10,260] [INFO] Query marker FASTA was written to OceanDNA-b30134/markers.fasta
[2023-03-17 02:04:10,260] [INFO] Task started: Blastn
[2023-03-17 02:04:10,260] [INFO] Running command: blastn -query OceanDNA-b30134/markers.fasta -db /var/lib/cwl/stg445760c5-303e-48c1-a8a8-a69c1565266f/dqc_reference/reference_markers.fasta -out OceanDNA-b30134/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:11,236] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:11,237] [INFO] Selected 22 target genomes.
[2023-03-17 02:04:11,237] [INFO] Target genome list was writen to OceanDNA-b30134/target_genomes.txt
[2023-03-17 02:04:11,251] [INFO] Task started: fastANI
[2023-03-17 02:04:11,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg40037c56-825e-4d36-ac44-6c640005326a/OceanDNA-b30134.fa --refList OceanDNA-b30134/target_genomes.txt --output OceanDNA-b30134/fastani_result.tsv --threads 1
[2023-03-17 02:04:28,438] [INFO] Task succeeded: fastANI
[2023-03-17 02:04:28,438] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg445760c5-303e-48c1-a8a8-a69c1565266f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:04:28,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg445760c5-303e-48c1-a8a8-a69c1565266f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:04:28,451] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:04:28,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:04:28,451] [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
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	83.0573	714	935	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	81.6201	678	935	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	80.8365	628	935	95	below_threshold
Roseovarius mucosus	strain=DSM 17069	GCA_000768555.3	215743	215743	type	True	79.6277	575	935	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	79.4882	511	935	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.2783	472	935	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	79.2196	424	935	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	79.2083	468	935	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	79.195	502	935	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.1898	489	935	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.0108	497	935	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	79.0019	474	935	95	below_threshold
Roseovarius aestuariivivens	strain=GHTF-24	GCA_004761875.1	1888910	1888910	type	True	78.8094	429	935	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.805	451	935	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.6929	478	935	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	78.5997	479	935	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	78.5898	384	935	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.3808	390	935	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.9449	351	935	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	77.8365	367	935	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	77.817	364	935	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.7599	359	935	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:04:28,451] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30134/tc_result.tsv
[2023-03-17 02:04:28,451] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:04:28,451] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:04:28,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg445760c5-303e-48c1-a8a8-a69c1565266f/dqc_reference/checkm_data
[2023-03-17 02:04:28,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:04:28,457] [INFO] Task started: CheckM
[2023-03-17 02:04:28,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30134/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30134/checkm_input OceanDNA-b30134/checkm_result
[2023-03-17 02:05:16,468] [INFO] Task succeeded: CheckM
[2023-03-17 02:05:16,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:05:16,471] [INFO] ===== Completeness check finished =====
[2023-03-17 02:05:16,471] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:05:16,472] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30134/markers.fasta)
[2023-03-17 02:05:16,473] [INFO] Task started: Blastn
[2023-03-17 02:05:16,473] [INFO] Running command: blastn -query OceanDNA-b30134/markers.fasta -db /var/lib/cwl/stg445760c5-303e-48c1-a8a8-a69c1565266f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30134/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:05:18,438] [INFO] Task succeeded: Blastn
[2023-03-17 02:05:18,439] [INFO] Selected 10 target genomes.
[2023-03-17 02:05:18,439] [INFO] Target genome list was writen to OceanDNA-b30134/target_genomes_gtdb.txt
[2023-03-17 02:05:18,731] [INFO] Task started: fastANI
[2023-03-17 02:05:18,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg40037c56-825e-4d36-ac44-6c640005326a/OceanDNA-b30134.fa --refList OceanDNA-b30134/target_genomes_gtdb.txt --output OceanDNA-b30134/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:05:25,872] [INFO] Task succeeded: fastANI
[2023-03-17 02:05:25,879] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:05:25,879] [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_002720475.1	s__Roseovarius sp002720475	99.7641	694	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	conclusive
GCA_014359765.1	s__Roseovarius sp014359765	85.7454	633	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842985.1	s__Roseovarius sp002842985	85.585	776	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428225.1	s__Roseovarius sp002428225	85.0722	477	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.12	96.12	0.88	0.88	2	-
GCF_018069895.1	s__Roseovarius sp018069895	84.6701	722	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.42	99.42	0.86	0.86	2	-
GCA_002421985.1	s__Roseovarius sp002421985	83.3849	592	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002925845.1	s__Roseovarius nitratireducens	83.0729	714	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.60	96.60	0.90	0.90	2	-
GCA_016278295.1	s__Roseovarius sp016278295	82.8437	594	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	81.6311	677	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_003651245.1	s__Roseovarius spongiae	79.5472	535	935	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:05:25,879] [INFO] GTDB search result was written to OceanDNA-b30134/result_gtdb.tsv
[2023-03-17 02:05:25,879] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:05:25,881] [INFO] DFAST_QC result json was written to OceanDNA-b30134/dqc_result.json
[2023-03-17 02:05:25,881] [INFO] DFAST_QC completed!
[2023-03-17 02:05:25,881] [INFO] Total running time: 0h1m35s