[2023-03-18 22:05:52,740] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:05:52,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:05:52,741] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e5d398e-3328-4946-b582-020ae500a17b/dqc_reference
[2023-03-18 22:05:55,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:05:55,263] [INFO] Task started: Prodigal
[2023-03-18 22:05:55,264] [INFO] Running command: cat /var/lib/cwl/stg14b50926-4011-4cde-b1f3-49860828e917/OceanDNA-b22092.fa | prodigal -d OceanDNA-b22092/cds.fna -a OceanDNA-b22092/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:06:04,146] [INFO] Task succeeded: Prodigal
[2023-03-18 22:06:04,146] [INFO] Task started: HMMsearch
[2023-03-18 22:06:04,146] [INFO] Running command: hmmsearch --tblout OceanDNA-b22092/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e5d398e-3328-4946-b582-020ae500a17b/dqc_reference/reference_markers.hmm OceanDNA-b22092/protein.faa > /dev/null
[2023-03-18 22:06:04,293] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:06:04,293] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg14b50926-4011-4cde-b1f3-49860828e917/OceanDNA-b22092.fa]
[2023-03-18 22:06:04,304] [INFO] Query marker FASTA was written to OceanDNA-b22092/markers.fasta
[2023-03-18 22:06:04,306] [INFO] Task started: Blastn
[2023-03-18 22:06:04,306] [INFO] Running command: blastn -query OceanDNA-b22092/markers.fasta -db /var/lib/cwl/stg4e5d398e-3328-4946-b582-020ae500a17b/dqc_reference/reference_markers.fasta -out OceanDNA-b22092/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:06:06,356] [INFO] Task succeeded: Blastn
[2023-03-18 22:06:06,357] [INFO] Selected 20 target genomes.
[2023-03-18 22:06:06,357] [INFO] Target genome list was writen to OceanDNA-b22092/target_genomes.txt
[2023-03-18 22:06:06,374] [INFO] Task started: fastANI
[2023-03-18 22:06:06,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg14b50926-4011-4cde-b1f3-49860828e917/OceanDNA-b22092.fa --refList OceanDNA-b22092/target_genomes.txt --output OceanDNA-b22092/fastani_result.tsv --threads 1
[2023-03-18 22:06:21,914] [INFO] Task succeeded: fastANI
[2023-03-18 22:06:21,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e5d398e-3328-4946-b582-020ae500a17b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:06:21,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e5d398e-3328-4946-b582-020ae500a17b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:06:21,925] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:06:21,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:06:21,926] [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
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	82.7801	265	297	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	82.7771	265	297	95	below_threshold
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	77.1338	96	297	95	below_threshold
Thermopolyspora flexuosa	strain=DSM 43186	GCA_006716785.1	103836	103836	type	True	74.974	54	297	95	below_threshold
Thermopolyspora flexuosa	strain=JCM 3056	GCA_014647775.1	103836	103836	type	True	74.9739	54	297	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	74.9311	51	297	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	74.7767	83	297	95	below_threshold
Frankia inefficax	strain=EuI1c	GCA_000166135.1	298654	298654	type	True	74.7585	63	297	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	74.7074	71	297	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	74.6819	66	297	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	74.6768	93	297	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_000716755.1	103733	103733	type	True	74.6768	93	297	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:06:21,926] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22092/tc_result.tsv
[2023-03-18 22:06:21,926] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:06:21,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:06:21,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e5d398e-3328-4946-b582-020ae500a17b/dqc_reference/checkm_data
[2023-03-18 22:06:21,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:06:21,943] [INFO] Task started: CheckM
[2023-03-18 22:06:21,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22092/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22092/checkm_input OceanDNA-b22092/checkm_result
[2023-03-18 22:06:47,956] [INFO] Task succeeded: CheckM
[2023-03-18 22:06:47,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.31%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:06:47,958] [INFO] ===== Completeness check finished =====
[2023-03-18 22:06:47,959] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:06:47,959] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22092/markers.fasta)
[2023-03-18 22:06:47,960] [INFO] Task started: Blastn
[2023-03-18 22:06:47,960] [INFO] Running command: blastn -query OceanDNA-b22092/markers.fasta -db /var/lib/cwl/stg4e5d398e-3328-4946-b582-020ae500a17b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22092/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:06:49,151] [INFO] Task succeeded: Blastn
[2023-03-18 22:06:49,152] [INFO] Selected 21 target genomes.
[2023-03-18 22:06:49,152] [INFO] Target genome list was writen to OceanDNA-b22092/target_genomes_gtdb.txt
[2023-03-18 22:06:49,324] [INFO] Task started: fastANI
[2023-03-18 22:06:49,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg14b50926-4011-4cde-b1f3-49860828e917/OceanDNA-b22092.fa --refList OceanDNA-b22092/target_genomes_gtdb.txt --output OceanDNA-b22092/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:07:02,243] [INFO] Task succeeded: fastANI
[2023-03-18 22:07:02,245] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:07:02,246] [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_000284115.1	s__Phycisphaera mikurensis	82.7801	265	297	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Phycisphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014207595.1	s__Algisphaera agarilytica	77.1366	95	297	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Algisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:07:02,246] [INFO] GTDB search result was written to OceanDNA-b22092/result_gtdb.tsv
[2023-03-18 22:07:02,246] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:07:02,247] [INFO] DFAST_QC result json was written to OceanDNA-b22092/dqc_result.json
[2023-03-18 22:07:02,247] [INFO] DFAST_QC completed!
[2023-03-18 22:07:02,247] [INFO] Total running time: 0h1m10s