[2023-03-17 13:01:52,509] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:52,509] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:52,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg91d67c95-6f7a-4027-8208-1b93578e62a6/dqc_reference
[2023-03-17 13:01:55,105] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:55,106] [INFO] Task started: Prodigal
[2023-03-17 13:01:55,106] [INFO] Running command: cat /var/lib/cwl/stg5e93293e-fc95-4f1a-bc42-e1a6459c6c2b/OceanDNA-b23937.fa | prodigal -d OceanDNA-b23937/cds.fna -a OceanDNA-b23937/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:14,183] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:14,184] [INFO] Task started: HMMsearch
[2023-03-17 13:02:14,184] [INFO] Running command: hmmsearch --tblout OceanDNA-b23937/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91d67c95-6f7a-4027-8208-1b93578e62a6/dqc_reference/reference_markers.hmm OceanDNA-b23937/protein.faa > /dev/null
[2023-03-17 13:02:14,389] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:14,389] [INFO] Found 6/6 markers.
[2023-03-17 13:02:14,409] [INFO] Query marker FASTA was written to OceanDNA-b23937/markers.fasta
[2023-03-17 13:02:14,409] [INFO] Task started: Blastn
[2023-03-17 13:02:14,409] [INFO] Running command: blastn -query OceanDNA-b23937/markers.fasta -db /var/lib/cwl/stg91d67c95-6f7a-4027-8208-1b93578e62a6/dqc_reference/reference_markers.fasta -out OceanDNA-b23937/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:15,171] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:15,171] [INFO] Selected 18 target genomes.
[2023-03-17 13:02:15,172] [INFO] Target genome list was writen to OceanDNA-b23937/target_genomes.txt
[2023-03-17 13:02:15,183] [INFO] Task started: fastANI
[2023-03-17 13:02:15,183] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e93293e-fc95-4f1a-bc42-e1a6459c6c2b/OceanDNA-b23937.fa --refList OceanDNA-b23937/target_genomes.txt --output OceanDNA-b23937/fastani_result.tsv --threads 1
[2023-03-17 13:02:26,353] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:26,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91d67c95-6f7a-4027-8208-1b93578e62a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:26,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91d67c95-6f7a-4027-8208-1b93578e62a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:26,363] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:26,363] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:02:26,363] [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
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	88.7973	860	1001	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	79.3065	524	1001	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	78.8436	486	1001	95	below_threshold
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.225	238	1001	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.6935	206	1001	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	76.6906	192	1001	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	76.6906	192	1001	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	76.6329	218	1001	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	76.6223	222	1001	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_012848855.1	1712261	1712261	type	True	76.2047	83	1001	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	76.2034	83	1001	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	76.1637	85	1001	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	75.7224	78	1001	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.1634	71	1001	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.1215	83	1001	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.088	71	1001	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:02:26,363] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23937/tc_result.tsv
[2023-03-17 13:02:26,363] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:26,364] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:26,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91d67c95-6f7a-4027-8208-1b93578e62a6/dqc_reference/checkm_data
[2023-03-17 13:02:26,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:26,368] [INFO] Task started: CheckM
[2023-03-17 13:02:26,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23937/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23937/checkm_input OceanDNA-b23937/checkm_result
[2023-03-17 13:03:19,848] [INFO] Task succeeded: CheckM
[2023-03-17 13:03:19,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:03:19,851] [INFO] ===== Completeness check finished =====
[2023-03-17 13:03:19,851] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:03:19,851] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23937/markers.fasta)
[2023-03-17 13:03:19,852] [INFO] Task started: Blastn
[2023-03-17 13:03:19,852] [INFO] Running command: blastn -query OceanDNA-b23937/markers.fasta -db /var/lib/cwl/stg91d67c95-6f7a-4027-8208-1b93578e62a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23937/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:03:21,399] [INFO] Task succeeded: Blastn
[2023-03-17 13:03:21,400] [INFO] Selected 11 target genomes.
[2023-03-17 13:03:21,400] [INFO] Target genome list was writen to OceanDNA-b23937/target_genomes_gtdb.txt
[2023-03-17 13:03:21,604] [INFO] Task started: fastANI
[2023-03-17 13:03:21,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e93293e-fc95-4f1a-bc42-e1a6459c6c2b/OceanDNA-b23937.fa --refList OceanDNA-b23937/target_genomes_gtdb.txt --output OceanDNA-b23937/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:03:28,948] [INFO] Task succeeded: fastANI
[2023-03-17 13:03:28,955] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:03:28,955] [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_900103475.1	s__Maricaulis salignorans	88.8072	859	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	79.2978	525	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCA_015665295.1	s__Maricaulis sp015665295	79.1919	502	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	78.9412	518	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014745.1	s__Maricaulis maris_A	78.9377	494	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCF_005871165.1	s__Maricaulis sp005871165	78.8345	487	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707795.1	s__Maricaulis sp002707795	78.793	364	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	99.42	99.36	0.71	0.69	3	-
GCF_016817355.1	s__Maricaulis parjimensis	78.7749	474	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480005.1	s__Maricaulis sp905480005	78.7469	428	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124665.1	s__Hyphobacterium sp016124665	77.3422	220	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848855.1	s__Pyruvatibacter mobilis	76.2047	83	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-03-17 13:03:28,956] [INFO] GTDB search result was written to OceanDNA-b23937/result_gtdb.tsv
[2023-03-17 13:03:28,956] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:03:28,957] [INFO] DFAST_QC result json was written to OceanDNA-b23937/dqc_result.json
[2023-03-17 13:03:28,957] [INFO] DFAST_QC completed!
[2023-03-17 13:03:28,957] [INFO] Total running time: 0h1m36s