[2023-03-15 08:59:47,082] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:47,082] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:47,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg4419ef84-46a5-44da-b65f-71aa0f728aca/dqc_reference
[2023-03-15 08:59:48,167] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:48,167] [INFO] Task started: Prodigal
[2023-03-15 08:59:48,168] [INFO] Running command: cat /var/lib/cwl/stg769516d2-b59e-4da3-8fbd-4f686d71b3ef/OceanDNA-b27542.fa | prodigal -d OceanDNA-b27542/cds.fna -a OceanDNA-b27542/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:04,176] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:04,177] [INFO] Task started: HMMsearch
[2023-03-15 09:00:04,177] [INFO] Running command: hmmsearch --tblout OceanDNA-b27542/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4419ef84-46a5-44da-b65f-71aa0f728aca/dqc_reference/reference_markers.hmm OceanDNA-b27542/protein.faa > /dev/null
[2023-03-15 09:00:04,394] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:04,395] [INFO] Found 6/6 markers.
[2023-03-15 09:00:04,417] [INFO] Query marker FASTA was written to OceanDNA-b27542/markers.fasta
[2023-03-15 09:00:04,417] [INFO] Task started: Blastn
[2023-03-15 09:00:04,417] [INFO] Running command: blastn -query OceanDNA-b27542/markers.fasta -db /var/lib/cwl/stg4419ef84-46a5-44da-b65f-71aa0f728aca/dqc_reference/reference_markers.fasta -out OceanDNA-b27542/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:05,248] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:05,249] [INFO] Selected 29 target genomes.
[2023-03-15 09:00:05,250] [INFO] Target genome list was writen to OceanDNA-b27542/target_genomes.txt
[2023-03-15 09:00:05,266] [INFO] Task started: fastANI
[2023-03-15 09:00:05,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg769516d2-b59e-4da3-8fbd-4f686d71b3ef/OceanDNA-b27542.fa --refList OceanDNA-b27542/target_genomes.txt --output OceanDNA-b27542/fastani_result.tsv --threads 1
[2023-03-15 09:00:25,371] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:25,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4419ef84-46a5-44da-b65f-71aa0f728aca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:25,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4419ef84-46a5-44da-b65f-71aa0f728aca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:25,387] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:25,387] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:00:25,387] [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 pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.2055	312	835	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.8878	301	835	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.8265	278	835	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.6979	239	835	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.6594	227	835	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.6259	230	835	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.6171	260	835	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.5844	276	835	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.5669	219	835	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.4746	228	835	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	77.4715	219	835	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	77.4091	248	835	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.3828	210	835	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	77.3776	246	835	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	77.3496	235	835	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.3383	201	835	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.2432	238	835	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.2365	223	835	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	77.1867	202	835	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	77.1582	183	835	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.1256	204	835	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	77.1042	186	835	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.0337	182	835	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	77.0024	162	835	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9445	155	835	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.944	185	835	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	76.508	163	835	95	below_threshold
Roseicitreum antarcticum	strain=CGMCC 1.8894	GCA_900107025.1	564137	564137	type	True	76.4872	164	835	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.4165	178	835	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:00:25,388] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27542/tc_result.tsv
[2023-03-15 09:00:25,388] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:25,388] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:25,388] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4419ef84-46a5-44da-b65f-71aa0f728aca/dqc_reference/checkm_data
[2023-03-15 09:00:25,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:25,393] [INFO] Task started: CheckM
[2023-03-15 09:00:25,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27542/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27542/checkm_input OceanDNA-b27542/checkm_result
[2023-03-15 09:01:07,917] [INFO] Task succeeded: CheckM
[2023-03-15 09:01:07,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.87%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 09:01:07,920] [INFO] ===== Completeness check finished =====
[2023-03-15 09:01:07,920] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:01:07,920] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27542/markers.fasta)
[2023-03-15 09:01:07,920] [INFO] Task started: Blastn
[2023-03-15 09:01:07,920] [INFO] Running command: blastn -query OceanDNA-b27542/markers.fasta -db /var/lib/cwl/stg4419ef84-46a5-44da-b65f-71aa0f728aca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27542/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:01:09,473] [INFO] Task succeeded: Blastn
[2023-03-15 09:01:09,473] [INFO] Selected 28 target genomes.
[2023-03-15 09:01:09,474] [INFO] Target genome list was writen to OceanDNA-b27542/target_genomes_gtdb.txt
[2023-03-15 09:01:09,517] [INFO] Task started: fastANI
[2023-03-15 09:01:09,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg769516d2-b59e-4da3-8fbd-4f686d71b3ef/OceanDNA-b27542.fa --refList OceanDNA-b27542/target_genomes_gtdb.txt --output OceanDNA-b27542/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:01:31,628] [INFO] Task succeeded: fastANI
[2023-03-15 09:01:31,643] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 09:01:31,644] [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_013214715.1	s__JABSSB01 sp013214715	99.1518	757	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSB01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001507595.1	s__Ruegeria marisrubri	77.8069	279	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031405.1	s__Ruegeria sp013031405	77.718	289	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	77.7027	237	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	77.6501	227	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172225.1	s__Ruegeria_E litorea	77.6428	228	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	77.6213	258	835	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_004358185.1	s__Antarcticimicrobium luteum	77.596	275	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013033515.1	s__Ruegeria sp013033515	77.5473	219	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.60	97.60	0.95	0.93	6	-
GCA_002366795.1	s__UBA3069 sp002366795	77.5291	187	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA3069	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032855.1	s__Ruegeria arenilitoris	77.4951	285	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.27	95.93	0.96	0.94	31	-
GCF_003008555.2	s__Pukyongiella litopenaei	77.4897	285	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013034685.1	s__Ruegeria lacuscaerulensis_B	77.4858	235	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.87	97.79	0.94	0.94	3	-
GCF_002210095.1	s__Marinibacterium profundimaris	77.4819	251	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.4746	228	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.3879	261	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_017743935.1	s__Ruegeria_E sp017743935	77.3753	245	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.375	206	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000590925.1	s__Roseicyclus elongatus	77.347	201	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014872875.1	s__WKFI01 sp014872875	77.3186	204	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WKFI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	77.3021	231	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001458395.1	s__Leisingera aquaemixtae	77.2432	238	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_004123675.1	s__Leisingera sp004123675	77.2333	218	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.03	97.97	0.88	0.88	3	-
GCF_000813745.1	s__Leisingera sp000813745	77.1722	230	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709405.1	s__Marinibacterium sp002709405	77.1445	220	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018145.1	s__Dinoroseobacter shibae	77.1375	182	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708925.1	s__Thalassobius sp002708925	77.0379	175	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
GCA_013373325.1	s__Leisingera sp013373325	76.651	174	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:01:31,644] [INFO] GTDB search result was written to OceanDNA-b27542/result_gtdb.tsv
[2023-03-15 09:01:31,644] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:01:31,647] [INFO] DFAST_QC result json was written to OceanDNA-b27542/dqc_result.json
[2023-03-15 09:01:31,647] [INFO] DFAST_QC completed!
[2023-03-15 09:01:31,647] [INFO] Total running time: 0h1m45s