[2023-03-16 07:22:13,561] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:22:13,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:22:13,561] [INFO] DQC Reference Directory: /var/lib/cwl/stge7761e31-19d9-47ab-9932-272bea526745/dqc_reference
[2023-03-16 07:22:14,666] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:22:14,666] [INFO] Task started: Prodigal
[2023-03-16 07:22:14,666] [INFO] Running command: cat /var/lib/cwl/stg954abf50-d51d-45e0-a79c-b8749a683a52/OceanDNA-b30149.fa | prodigal -d OceanDNA-b30149/cds.fna -a OceanDNA-b30149/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:22:33,593] [INFO] Task succeeded: Prodigal
[2023-03-16 07:22:33,594] [INFO] Task started: HMMsearch
[2023-03-16 07:22:33,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b30149/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7761e31-19d9-47ab-9932-272bea526745/dqc_reference/reference_markers.hmm OceanDNA-b30149/protein.faa > /dev/null
[2023-03-16 07:22:33,786] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:22:33,786] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg954abf50-d51d-45e0-a79c-b8749a683a52/OceanDNA-b30149.fa]
[2023-03-16 07:22:33,813] [INFO] Query marker FASTA was written to OceanDNA-b30149/markers.fasta
[2023-03-16 07:22:33,814] [INFO] Task started: Blastn
[2023-03-16 07:22:33,814] [INFO] Running command: blastn -query OceanDNA-b30149/markers.fasta -db /var/lib/cwl/stge7761e31-19d9-47ab-9932-272bea526745/dqc_reference/reference_markers.fasta -out OceanDNA-b30149/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:22:34,333] [INFO] Task succeeded: Blastn
[2023-03-16 07:22:34,334] [INFO] Selected 10 target genomes.
[2023-03-16 07:22:34,334] [INFO] Target genome list was writen to OceanDNA-b30149/target_genomes.txt
[2023-03-16 07:22:34,340] [INFO] Task started: fastANI
[2023-03-16 07:22:34,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg954abf50-d51d-45e0-a79c-b8749a683a52/OceanDNA-b30149.fa --refList OceanDNA-b30149/target_genomes.txt --output OceanDNA-b30149/fastani_result.tsv --threads 1
[2023-03-16 07:22:43,260] [INFO] Task succeeded: fastANI
[2023-03-16 07:22:43,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7761e31-19d9-47ab-9932-272bea526745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:22:43,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7761e31-19d9-47ab-9932-272bea526745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:22:43,268] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:22:43,268] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:22:43,269] [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
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	87.9975	786	926	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	87.988	783	926	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	81.5203	583	926	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	81.0328	559	926	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	80.5745	503	926	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	80.0218	520	926	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.5035	401	926	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.4395	259	926	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.2447	195	926	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.8095	190	926	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:22:43,269] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30149/tc_result.tsv
[2023-03-16 07:22:43,269] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:22:43,269] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:22:43,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7761e31-19d9-47ab-9932-272bea526745/dqc_reference/checkm_data
[2023-03-16 07:22:43,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:22:43,512] [INFO] Task started: CheckM
[2023-03-16 07:22:43,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30149/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30149/checkm_input OceanDNA-b30149/checkm_result
[2023-03-16 07:23:29,370] [INFO] Task succeeded: CheckM
[2023-03-16 07:23:29,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:23:29,374] [INFO] ===== Completeness check finished =====
[2023-03-16 07:23:29,374] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:23:29,374] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30149/markers.fasta)
[2023-03-16 07:23:29,375] [INFO] Task started: Blastn
[2023-03-16 07:23:29,375] [INFO] Running command: blastn -query OceanDNA-b30149/markers.fasta -db /var/lib/cwl/stge7761e31-19d9-47ab-9932-272bea526745/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30149/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:23:30,003] [INFO] Task succeeded: Blastn
[2023-03-16 07:23:30,004] [INFO] Selected 5 target genomes.
[2023-03-16 07:23:30,004] [INFO] Target genome list was writen to OceanDNA-b30149/target_genomes_gtdb.txt
[2023-03-16 07:23:30,179] [INFO] Task started: fastANI
[2023-03-16 07:23:30,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg954abf50-d51d-45e0-a79c-b8749a683a52/OceanDNA-b30149.fa --refList OceanDNA-b30149/target_genomes_gtdb.txt --output OceanDNA-b30149/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:23:35,614] [INFO] Task succeeded: fastANI
[2023-03-16 07:23:35,618] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:23:35,618] [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_003111685.1	s__Salipiger pacificus_A	96.4007	867	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	conclusive
GCF_002300555.1	s__Salipiger sp002300555	89.7049	638	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	87.988	783	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015223355.1	s__Salipiger pacificus_B	87.69	778	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	85.4013	703	926	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:23:35,619] [INFO] GTDB search result was written to OceanDNA-b30149/result_gtdb.tsv
[2023-03-16 07:23:35,619] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:23:35,620] [INFO] DFAST_QC result json was written to OceanDNA-b30149/dqc_result.json
[2023-03-16 07:23:35,620] [INFO] DFAST_QC completed!
[2023-03-16 07:23:35,620] [INFO] Total running time: 0h1m22s