[2023-03-16 19:07:15,843] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:07:15,843] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:07:15,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e82b909-5b75-4681-9b5c-7f4f6ef75e1d/dqc_reference
[2023-03-16 19:07:17,016] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:07:17,016] [INFO] Task started: Prodigal
[2023-03-16 19:07:17,017] [INFO] Running command: cat /var/lib/cwl/stg7b89c694-7356-4b29-afc0-0273d71fc904/OceanDNA-b27576.fa | prodigal -d OceanDNA-b27576/cds.fna -a OceanDNA-b27576/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:07:39,107] [INFO] Task succeeded: Prodigal
[2023-03-16 19:07:39,107] [INFO] Task started: HMMsearch
[2023-03-16 19:07:39,107] [INFO] Running command: hmmsearch --tblout OceanDNA-b27576/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e82b909-5b75-4681-9b5c-7f4f6ef75e1d/dqc_reference/reference_markers.hmm OceanDNA-b27576/protein.faa > /dev/null
[2023-03-16 19:07:39,308] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:07:39,309] [INFO] Found 6/6 markers.
[2023-03-16 19:07:39,333] [INFO] Query marker FASTA was written to OceanDNA-b27576/markers.fasta
[2023-03-16 19:07:39,334] [INFO] Task started: Blastn
[2023-03-16 19:07:39,335] [INFO] Running command: blastn -query OceanDNA-b27576/markers.fasta -db /var/lib/cwl/stg9e82b909-5b75-4681-9b5c-7f4f6ef75e1d/dqc_reference/reference_markers.fasta -out OceanDNA-b27576/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:07:40,199] [INFO] Task succeeded: Blastn
[2023-03-16 19:07:40,202] [INFO] Selected 27 target genomes.
[2023-03-16 19:07:40,202] [INFO] Target genome list was writen to OceanDNA-b27576/target_genomes.txt
[2023-03-16 19:07:40,213] [INFO] Task started: fastANI
[2023-03-16 19:07:40,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b89c694-7356-4b29-afc0-0273d71fc904/OceanDNA-b27576.fa --refList OceanDNA-b27576/target_genomes.txt --output OceanDNA-b27576/fastani_result.tsv --threads 1
[2023-03-16 19:08:00,430] [INFO] Task succeeded: fastANI
[2023-03-16 19:08:00,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e82b909-5b75-4681-9b5c-7f4f6ef75e1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:08:00,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e82b909-5b75-4681-9b5c-7f4f6ef75e1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:08:00,452] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:08:00,452] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:08:00,453] [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
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.4367	528	1142	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.3949	575	1142	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.3028	559	1142	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.2736	536	1142	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.2722	532	1142	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.1613	568	1142	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.9517	503	1142	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.8799	520	1142	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.8158	483	1142	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.7563	485	1142	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.3573	426	1142	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	78.3299	465	1142	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.1537	415	1142	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	78.0152	368	1142	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	77.9931	372	1142	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	77.8118	394	1142	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.7872	412	1142	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.7166	419	1142	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.6338	309	1142	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.4639	274	1142	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.4389	258	1142	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	77.3897	289	1142	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3136	275	1142	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	77.3125	282	1142	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	77.2754	282	1142	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.1498	258	1142	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.0327	266	1142	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:08:00,454] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27576/tc_result.tsv
[2023-03-16 19:08:00,455] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:08:00,455] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:08:00,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e82b909-5b75-4681-9b5c-7f4f6ef75e1d/dqc_reference/checkm_data
[2023-03-16 19:08:00,456] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:08:00,559] [INFO] Task started: CheckM
[2023-03-16 19:08:00,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27576/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27576/checkm_input OceanDNA-b27576/checkm_result
[2023-03-16 19:09:04,646] [INFO] Task succeeded: CheckM
[2023-03-16 19:09:04,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.99%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 19:09:04,653] [INFO] ===== Completeness check finished =====
[2023-03-16 19:09:04,653] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:09:04,653] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27576/markers.fasta)
[2023-03-16 19:09:04,655] [INFO] Task started: Blastn
[2023-03-16 19:09:04,655] [INFO] Running command: blastn -query OceanDNA-b27576/markers.fasta -db /var/lib/cwl/stg9e82b909-5b75-4681-9b5c-7f4f6ef75e1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27576/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:09:07,659] [INFO] Task succeeded: Blastn
[2023-03-16 19:09:07,661] [INFO] Selected 30 target genomes.
[2023-03-16 19:09:07,661] [INFO] Target genome list was writen to OceanDNA-b27576/target_genomes_gtdb.txt
[2023-03-16 19:09:07,727] [INFO] Task started: fastANI
[2023-03-16 19:09:07,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b89c694-7356-4b29-afc0-0273d71fc904/OceanDNA-b27576.fa --refList OceanDNA-b27576/target_genomes_gtdb.txt --output OceanDNA-b27576/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:09:33,448] [INFO] Task succeeded: fastANI
[2023-03-16 19:09:33,465] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 19:09:33,466] [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_900129345.1	s__Ruegeria intermedia	79.4406	527	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	79.3699	578	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_001507595.1	s__Ruegeria marisrubri	79.3031	559	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.2646	537	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.2039	512	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.161	568	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500245.1	s__Ruegeria_B sp010500245	79.1106	549	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	79.106	563	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	79.0303	464	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_001458395.1	s__Leisingera aquaemixtae	78.9519	502	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_900108275.1	s__Jhaorihella thermophila	78.8998	518	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	78.8728	512	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	78.8406	365	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	78.7878	473	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_009857745.1	s__Thalassobius mangrovi	78.7464	485	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	78.6405	469	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813725.1	s__Leisingera sp000813725	78.5656	452	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813965.1	s__Leisingera sp000813965	78.5371	431	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	78.3327	431	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_018219815.1	s__Thalassobius aquimarinus	78.3134	467	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016521575.1	s__Sedimentitalea sp016521575	78.2008	366	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	78.1538	415	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCA_002709405.1	s__Marinibacterium sp002709405	78.0907	422	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	78.0511	429	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	78.0247	367	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.9028	414	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	77.8695	366	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765275.1	s__Chachezhania sp009765275	77.7938	396	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.7656	414	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_001650875.1	s__Sulfitobacter sp001650875	77.7353	412	1142	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:09:33,466] [INFO] GTDB search result was written to OceanDNA-b27576/result_gtdb.tsv
[2023-03-16 19:09:33,466] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:09:33,469] [INFO] DFAST_QC result json was written to OceanDNA-b27576/dqc_result.json
[2023-03-16 19:09:33,469] [INFO] DFAST_QC completed!
[2023-03-16 19:09:33,469] [INFO] Total running time: 0h2m18s