[2023-03-15 04:15:08,920] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:15:08,920] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:15:08,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg98f4d6a7-1e57-4862-9b7f-f9bae8221292/dqc_reference
[2023-03-15 04:15:10,001] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:15:10,002] [INFO] Task started: Prodigal
[2023-03-15 04:15:10,002] [INFO] Running command: cat /var/lib/cwl/stgde36af27-d5fe-4e43-bf4b-e7880eccfedc/OceanDNA-b30076.fa | prodigal -d OceanDNA-b30076/cds.fna -a OceanDNA-b30076/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:15:19,686] [INFO] Task succeeded: Prodigal
[2023-03-15 04:15:19,686] [INFO] Task started: HMMsearch
[2023-03-15 04:15:19,686] [INFO] Running command: hmmsearch --tblout OceanDNA-b30076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98f4d6a7-1e57-4862-9b7f-f9bae8221292/dqc_reference/reference_markers.hmm OceanDNA-b30076/protein.faa > /dev/null
[2023-03-15 04:15:19,831] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:15:19,831] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgde36af27-d5fe-4e43-bf4b-e7880eccfedc/OceanDNA-b30076.fa]
[2023-03-15 04:15:19,846] [INFO] Query marker FASTA was written to OceanDNA-b30076/markers.fasta
[2023-03-15 04:15:19,847] [INFO] Task started: Blastn
[2023-03-15 04:15:19,848] [INFO] Running command: blastn -query OceanDNA-b30076/markers.fasta -db /var/lib/cwl/stg98f4d6a7-1e57-4862-9b7f-f9bae8221292/dqc_reference/reference_markers.fasta -out OceanDNA-b30076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:15:20,500] [INFO] Task succeeded: Blastn
[2023-03-15 04:15:20,500] [INFO] Selected 23 target genomes.
[2023-03-15 04:15:20,501] [INFO] Target genome list was writen to OceanDNA-b30076/target_genomes.txt
[2023-03-15 04:15:20,534] [INFO] Task started: fastANI
[2023-03-15 04:15:20,534] [INFO] Running command: fastANI --query /var/lib/cwl/stgde36af27-d5fe-4e43-bf4b-e7880eccfedc/OceanDNA-b30076.fa --refList OceanDNA-b30076/target_genomes.txt --output OceanDNA-b30076/fastani_result.tsv --threads 1
[2023-03-15 04:15:35,815] [INFO] Task succeeded: fastANI
[2023-03-15 04:15:35,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98f4d6a7-1e57-4862-9b7f-f9bae8221292/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:15:35,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98f4d6a7-1e57-4862-9b7f-f9bae8221292/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:15:35,828] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:15:35,828] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:15:35,828] [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 nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	78.5922	260	502	95	below_threshold
Roseovarius faecimaris	strain=MME-070	GCA_009762325.1	2494550	2494550	type	True	77.9234	224	502	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	77.8526	195	502	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	77.8418	193	502	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.8354	162	502	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	77.7712	186	502	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	77.6505	204	502	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.5928	176	502	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	77.5248	210	502	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.5003	206	502	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.4524	210	502	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.3859	155	502	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.1341	147	502	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.1121	137	502	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.8952	119	502	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.8575	119	502	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	76.8529	113	502	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	76.8523	112	502	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.8456	130	502	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.6003	105	502	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.4887	94	502	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.2435	95	502	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:15:35,829] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30076/tc_result.tsv
[2023-03-15 04:15:35,829] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:15:35,829] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:15:35,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98f4d6a7-1e57-4862-9b7f-f9bae8221292/dqc_reference/checkm_data
[2023-03-15 04:15:35,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:15:35,833] [INFO] Task started: CheckM
[2023-03-15 04:15:35,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30076/checkm_input OceanDNA-b30076/checkm_result
[2023-03-15 04:16:05,469] [INFO] Task succeeded: CheckM
[2023-03-15 04:16:05,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:16:05,474] [INFO] ===== Completeness check finished =====
[2023-03-15 04:16:05,474] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:16:05,475] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30076/markers.fasta)
[2023-03-15 04:16:05,476] [INFO] Task started: Blastn
[2023-03-15 04:16:05,476] [INFO] Running command: blastn -query OceanDNA-b30076/markers.fasta -db /var/lib/cwl/stg98f4d6a7-1e57-4862-9b7f-f9bae8221292/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:16:06,597] [INFO] Task succeeded: Blastn
[2023-03-15 04:16:06,601] [INFO] Selected 21 target genomes.
[2023-03-15 04:16:06,601] [INFO] Target genome list was writen to OceanDNA-b30076/target_genomes_gtdb.txt
[2023-03-15 04:16:06,629] [INFO] Task started: fastANI
[2023-03-15 04:16:06,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgde36af27-d5fe-4e43-bf4b-e7880eccfedc/OceanDNA-b30076.fa --refList OceanDNA-b30076/target_genomes_gtdb.txt --output OceanDNA-b30076/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:16:21,131] [INFO] Task succeeded: fastANI
[2023-03-15 04:16:21,142] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:16:21,143] [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_000152625.1	s__Roseovarius nubinhibens	78.5913	260	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_009762325.1	s__Roseovarius faecimaris	77.9234	224	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	77.8905	223	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	77.8603	212	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_900172255.1	s__Roseovarius halotolerans	77.8526	195	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.8355	162	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	77.7885	185	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_900142665.1	s__Roseovarius pacificus	77.773	178	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_001441615.1	s__Roseovarius atlanticus	77.6656	203	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363715.1	s__Roseovarius sp009363715	77.66	195	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	77.6106	175	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	77.3856	155	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	77.2876	140	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	77.1717	155	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.1341	147	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	77.0547	154	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792425.1	s__Thalassobius sp017792425	77.0492	119	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	76.8952	119	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_003335585.1	s__Sulfitobacter sp003335585	76.8776	143	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100085.1	s__Salipiger marinus	76.8456	130	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCA_003254465.1	s__Fluviibacterium sp003254465	76.5022	87	502	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:16:21,144] [INFO] GTDB search result was written to OceanDNA-b30076/result_gtdb.tsv
[2023-03-15 04:16:21,146] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:16:21,150] [INFO] DFAST_QC result json was written to OceanDNA-b30076/dqc_result.json
[2023-03-15 04:16:21,150] [INFO] DFAST_QC completed!
[2023-03-15 04:16:21,150] [INFO] Total running time: 0h1m12s