[2023-03-16 12:14:11,044] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:14:11,058] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:14:11,058] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0734bbb-9989-4f1a-92de-8a19d23d17fa/dqc_reference
[2023-03-16 12:14:13,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:14:13,631] [INFO] Task started: Prodigal
[2023-03-16 12:14:13,631] [INFO] Running command: cat /var/lib/cwl/stg69e23e28-87de-4a2b-8269-0f393ee9ec9c/OceanDNA-b29384.fa | prodigal -d OceanDNA-b29384/cds.fna -a OceanDNA-b29384/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:14:23,454] [INFO] Task succeeded: Prodigal
[2023-03-16 12:14:23,454] [INFO] Task started: HMMsearch
[2023-03-16 12:14:23,454] [INFO] Running command: hmmsearch --tblout OceanDNA-b29384/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0734bbb-9989-4f1a-92de-8a19d23d17fa/dqc_reference/reference_markers.hmm OceanDNA-b29384/protein.faa > /dev/null
[2023-03-16 12:14:23,620] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:14:23,621] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg69e23e28-87de-4a2b-8269-0f393ee9ec9c/OceanDNA-b29384.fa]
[2023-03-16 12:14:23,639] [INFO] Query marker FASTA was written to OceanDNA-b29384/markers.fasta
[2023-03-16 12:14:23,639] [INFO] Task started: Blastn
[2023-03-16 12:14:23,640] [INFO] Running command: blastn -query OceanDNA-b29384/markers.fasta -db /var/lib/cwl/stgc0734bbb-9989-4f1a-92de-8a19d23d17fa/dqc_reference/reference_markers.fasta -out OceanDNA-b29384/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:14:24,300] [INFO] Task succeeded: Blastn
[2023-03-16 12:14:24,301] [INFO] Selected 24 target genomes.
[2023-03-16 12:14:24,301] [INFO] Target genome list was writen to OceanDNA-b29384/target_genomes.txt
[2023-03-16 12:14:24,315] [INFO] Task started: fastANI
[2023-03-16 12:14:24,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg69e23e28-87de-4a2b-8269-0f393ee9ec9c/OceanDNA-b29384.fa --refList OceanDNA-b29384/target_genomes.txt --output OceanDNA-b29384/fastani_result.tsv --threads 1
[2023-03-16 12:14:40,635] [INFO] Task succeeded: fastANI
[2023-03-16 12:14:40,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0734bbb-9989-4f1a-92de-8a19d23d17fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:14:40,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0734bbb-9989-4f1a-92de-8a19d23d17fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:14:40,673] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:14:40,673] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 12:14:40,673] [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
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	78.8912	301	506	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.5941	258	506	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	77.5718	189	506	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	77.5475	219	506	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	77.5303	189	506	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	77.4273	189	506	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	77.4173	220	506	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	77.3748	210	506	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	77.3328	210	506	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	77.2459	206	506	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.2396	166	506	95	below_threshold
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	77.2095	204	506	95	below_threshold
[Luteovulum] sphaeroides subsp. megalophilum	strain=DSM 18937	GCA_900188265.1	418630	1063	type	True	77.0951	196	506	95	below_threshold
Meinhardsimonia xiamenensis	strain=CGMCC 1.10789	GCA_900102905.1	990712	990712	type	True	77.0419	172	506	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	77.0054	174	506	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	76.9464	192	506	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.909	155	506	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.884	145	506	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	76.6948	216	506	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	76.6899	139	506	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.6625	122	506	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.4655	139	506	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.4504	140	506	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	76.3915	168	506	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 12:14:40,673] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29384/tc_result.tsv
[2023-03-16 12:14:40,673] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:14:40,673] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:14:40,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0734bbb-9989-4f1a-92de-8a19d23d17fa/dqc_reference/checkm_data
[2023-03-16 12:14:40,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:14:40,678] [INFO] Task started: CheckM
[2023-03-16 12:14:40,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29384/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29384/checkm_input OceanDNA-b29384/checkm_result
[2023-03-16 12:15:14,431] [INFO] Task succeeded: CheckM
[2023-03-16 12:15:14,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.97%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 12:15:14,434] [INFO] ===== Completeness check finished =====
[2023-03-16 12:15:14,434] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:15:14,434] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29384/markers.fasta)
[2023-03-16 12:15:14,435] [INFO] Task started: Blastn
[2023-03-16 12:15:14,435] [INFO] Running command: blastn -query OceanDNA-b29384/markers.fasta -db /var/lib/cwl/stgc0734bbb-9989-4f1a-92de-8a19d23d17fa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29384/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:15:15,478] [INFO] Task succeeded: Blastn
[2023-03-16 12:15:15,479] [INFO] Selected 22 target genomes.
[2023-03-16 12:15:15,479] [INFO] Target genome list was writen to OceanDNA-b29384/target_genomes_gtdb.txt
[2023-03-16 12:15:15,767] [INFO] Task started: fastANI
[2023-03-16 12:15:15,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg69e23e28-87de-4a2b-8269-0f393ee9ec9c/OceanDNA-b29384.fa --refList OceanDNA-b29384/target_genomes_gtdb.txt --output OceanDNA-b29384/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:15:35,524] [INFO] Task succeeded: fastANI
[2023-03-16 12:15:35,536] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:15:35,536] [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_003003095.1	s__Hasllibacter halocynthiae	78.8411	304	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820245.1	s__Jannaschia sp016820245	78.057	262	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	77.8656	250	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	77.6079	257	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172345.1	s__Limimaricola soesokkakensis	77.5398	191	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	77.4807	218	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404595.1	s__Jannaschia marina	77.4445	218	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	77.4432	188	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
GCA_004005435.1	s__CCMM004 sp004005435	77.4127	229	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314685.1	s__HLUCCA09 sp001314685	77.3206	241	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	77.3061	212	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.2434	190	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521785.1	s__Roseivivax halodurans	77.2095	204	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000743715.1	s__Palleronia rufa	77.2069	168	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188335.1	s__Tropicimonas sediminicola	77.1954	173	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172355.1	s__Oceanicola antarcticus	77.0366	170	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	76.9583	152	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217255.1	s__Pseudoroseicyclus aestuarii	76.9451	192	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842835.1	s__PHEG01 sp002842835	76.9031	95	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PHEG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017993425.1	s__Amaricoccus sp017993425	76.7479	240	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001078595.1	s__Rhodobacter_B lobularis	76.6519	135	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	76.552	133	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:15:35,537] [INFO] GTDB search result was written to OceanDNA-b29384/result_gtdb.tsv
[2023-03-16 12:15:35,537] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:15:35,543] [INFO] DFAST_QC result json was written to OceanDNA-b29384/dqc_result.json
[2023-03-16 12:15:35,543] [INFO] DFAST_QC completed!
[2023-03-16 12:15:35,543] [INFO] Total running time: 0h1m24s