[2023-03-16 06:12:59,358] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:12:59,359] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:12:59,359] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6750f20-dbf9-44c2-ba5d-e58506e2d77b/dqc_reference
[2023-03-16 06:13:00,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:13:00,469] [INFO] Task started: Prodigal
[2023-03-16 06:13:00,469] [INFO] Running command: cat /var/lib/cwl/stg39f99ddc-cca5-4f87-8dc2-de3bfbcc56a7/OceanDNA-b30571.fa | prodigal -d OceanDNA-b30571/cds.fna -a OceanDNA-b30571/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:13:09,333] [INFO] Task succeeded: Prodigal
[2023-03-16 06:13:09,333] [INFO] Task started: HMMsearch
[2023-03-16 06:13:09,333] [INFO] Running command: hmmsearch --tblout OceanDNA-b30571/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6750f20-dbf9-44c2-ba5d-e58506e2d77b/dqc_reference/reference_markers.hmm OceanDNA-b30571/protein.faa > /dev/null
[2023-03-16 06:13:09,487] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:13:09,488] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg39f99ddc-cca5-4f87-8dc2-de3bfbcc56a7/OceanDNA-b30571.fa]
[2023-03-16 06:13:09,504] [INFO] Query marker FASTA was written to OceanDNA-b30571/markers.fasta
[2023-03-16 06:13:09,504] [INFO] Task started: Blastn
[2023-03-16 06:13:09,504] [INFO] Running command: blastn -query OceanDNA-b30571/markers.fasta -db /var/lib/cwl/stgb6750f20-dbf9-44c2-ba5d-e58506e2d77b/dqc_reference/reference_markers.fasta -out OceanDNA-b30571/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:10,078] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:10,079] [INFO] Selected 14 target genomes.
[2023-03-16 06:13:10,079] [INFO] Target genome list was writen to OceanDNA-b30571/target_genomes.txt
[2023-03-16 06:13:10,086] [INFO] Task started: fastANI
[2023-03-16 06:13:10,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f99ddc-cca5-4f87-8dc2-de3bfbcc56a7/OceanDNA-b30571.fa --refList OceanDNA-b30571/target_genomes.txt --output OceanDNA-b30571/fastani_result.tsv --threads 1
[2023-03-16 06:13:19,091] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:19,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6750f20-dbf9-44c2-ba5d-e58506e2d77b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:13:19,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6750f20-dbf9-44c2-ba5d-e58506e2d77b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:13:19,106] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:13:19,106] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:13:19,106] [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
Tritonibacter scottomollicae	strain=DSM 25328	GCA_003003215.1	483013	483013	type	True	80.5691	188	334	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	80.3407	175	334	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	80.3042	176	334	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.8178	123	334	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	78.4253	131	334	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	78.3994	121	334	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	78.3947	132	334	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.0526	132	334	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	78.0031	108	334	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.6404	95	334	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.6206	53	334	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:13:19,107] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30571/tc_result.tsv
[2023-03-16 06:13:19,107] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:13:19,107] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:13:19,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6750f20-dbf9-44c2-ba5d-e58506e2d77b/dqc_reference/checkm_data
[2023-03-16 06:13:19,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:13:19,111] [INFO] Task started: CheckM
[2023-03-16 06:13:19,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30571/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30571/checkm_input OceanDNA-b30571/checkm_result
[2023-03-16 06:13:46,055] [INFO] Task succeeded: CheckM
[2023-03-16 06:13:46,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.98%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:13:46,058] [INFO] ===== Completeness check finished =====
[2023-03-16 06:13:46,058] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:13:46,058] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30571/markers.fasta)
[2023-03-16 06:13:46,059] [INFO] Task started: Blastn
[2023-03-16 06:13:46,060] [INFO] Running command: blastn -query OceanDNA-b30571/markers.fasta -db /var/lib/cwl/stgb6750f20-dbf9-44c2-ba5d-e58506e2d77b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30571/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:47,055] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:47,056] [INFO] Selected 13 target genomes.
[2023-03-16 06:13:47,056] [INFO] Target genome list was writen to OceanDNA-b30571/target_genomes_gtdb.txt
[2023-03-16 06:13:47,068] [INFO] Task started: fastANI
[2023-03-16 06:13:47,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f99ddc-cca5-4f87-8dc2-de3bfbcc56a7/OceanDNA-b30571.fa --refList OceanDNA-b30571/target_genomes_gtdb.txt --output OceanDNA-b30571/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:13:55,803] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:55,811] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:13:55,811] [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_003003215.1	s__Epibacterium scottomollicae	80.5691	188	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806385.1	s__Epibacterium sp011806385	80.3499	184	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001681715.1	s__Epibacterium mobile	80.3407	175	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	97.01	96.41	0.91	0.87	56	-
GCF_001518015.1	s__Epibacterium horizontis	80.0285	191	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014065.1	s__Epibacterium sp000014065	79.7633	169	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	78.7822	124	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_001458415.1	s__Epibacterium multivorans	78.4253	131	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013317235.1	s__Leisingera sp013317235	78.4156	127	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473325.1	s__Leisingera caerulea	78.3994	121	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813745.1	s__Leisingera sp000813745	78.3333	112	334	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	78.2804	114	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	78.1557	126	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCA_013373325.1	s__Leisingera sp013373325	77.5265	116	334	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:13:55,812] [INFO] GTDB search result was written to OceanDNA-b30571/result_gtdb.tsv
[2023-03-16 06:13:55,812] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:13:55,814] [INFO] DFAST_QC result json was written to OceanDNA-b30571/dqc_result.json
[2023-03-16 06:13:55,814] [INFO] DFAST_QC completed!
[2023-03-16 06:13:55,814] [INFO] Total running time: 0h0m56s