[2023-03-16 03:23:48,507] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:48,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:48,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg27f8f9c5-dead-43d5-9706-c121122133a3/dqc_reference
[2023-03-16 03:23:50,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,651] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,651] [INFO] Running command: cat /var/lib/cwl/stge61eb930-00f9-4f15-bea0-98cf31ef9e8a/OceanDNA-b2665.fa | prodigal -d OceanDNA-b2665/cds.fna -a OceanDNA-b2665/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:24:06,010] [INFO] Task succeeded: Prodigal
[2023-03-16 03:24:06,011] [INFO] Task started: HMMsearch
[2023-03-16 03:24:06,011] [INFO] Running command: hmmsearch --tblout OceanDNA-b2665/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27f8f9c5-dead-43d5-9706-c121122133a3/dqc_reference/reference_markers.hmm OceanDNA-b2665/protein.faa > /dev/null
[2023-03-16 03:24:06,259] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:24:06,260] [INFO] Found 6/6 markers.
[2023-03-16 03:24:06,277] [INFO] Query marker FASTA was written to OceanDNA-b2665/markers.fasta
[2023-03-16 03:24:06,277] [INFO] Task started: Blastn
[2023-03-16 03:24:06,277] [INFO] Running command: blastn -query OceanDNA-b2665/markers.fasta -db /var/lib/cwl/stg27f8f9c5-dead-43d5-9706-c121122133a3/dqc_reference/reference_markers.fasta -out OceanDNA-b2665/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:07,384] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:07,385] [INFO] Selected 11 target genomes.
[2023-03-16 03:24:07,385] [INFO] Target genome list was writen to OceanDNA-b2665/target_genomes.txt
[2023-03-16 03:24:07,392] [INFO] Task started: fastANI
[2023-03-16 03:24:07,392] [INFO] Running command: fastANI --query /var/lib/cwl/stge61eb930-00f9-4f15-bea0-98cf31ef9e8a/OceanDNA-b2665.fa --refList OceanDNA-b2665/target_genomes.txt --output OceanDNA-b2665/fastani_result.tsv --threads 1
[2023-03-16 03:24:14,596] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:14,597] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27f8f9c5-dead-43d5-9706-c121122133a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:14,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27f8f9c5-dead-43d5-9706-c121122133a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:14,605] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:14,605] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:24:14,605] [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
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	94.1815	707	811	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	85.3247	612	811	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	85.169	620	811	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	81.0583	471	811	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	81.0477	453	811	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	78.9918	343	811	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	78.6764	352	811	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.6393	330	811	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	78.6094	317	811	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.4892	297	811	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.4013	314	811	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:14,605] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2665/tc_result.tsv
[2023-03-16 03:24:14,605] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:14,605] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:14,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27f8f9c5-dead-43d5-9706-c121122133a3/dqc_reference/checkm_data
[2023-03-16 03:24:14,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:14,611] [INFO] Task started: CheckM
[2023-03-16 03:24:14,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2665/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2665/checkm_input OceanDNA-b2665/checkm_result
[2023-03-16 03:24:54,723] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:54,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:54,726] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:54,726] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:54,726] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2665/markers.fasta)
[2023-03-16 03:24:54,726] [INFO] Task started: Blastn
[2023-03-16 03:24:54,726] [INFO] Running command: blastn -query OceanDNA-b2665/markers.fasta -db /var/lib/cwl/stg27f8f9c5-dead-43d5-9706-c121122133a3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2665/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:56,505] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:56,506] [INFO] Selected 10 target genomes.
[2023-03-16 03:24:56,506] [INFO] Target genome list was writen to OceanDNA-b2665/target_genomes_gtdb.txt
[2023-03-16 03:24:56,624] [INFO] Task started: fastANI
[2023-03-16 03:24:56,624] [INFO] Running command: fastANI --query /var/lib/cwl/stge61eb930-00f9-4f15-bea0-98cf31ef9e8a/OceanDNA-b2665.fa --refList OceanDNA-b2665/target_genomes_gtdb.txt --output OceanDNA-b2665/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:25:02,288] [INFO] Task succeeded: fastANI
[2023-03-16 03:25:02,295] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:25:02,295] [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_002355395.1	s__Microcella alkaliphila_A	97.5744	725	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004216855.1	s__Microcella alkaliphila	94.1815	707	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216575.1	s__Microcella putealis	85.2896	614	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microcella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	81.9029	497	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425665.1	s__Yonghaparkia sp001425665	81.5762	479	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	99.25	99.25	0.97	0.97	2	-
GCA_012530535.1	s__Yonghaparkia sp012530535	81.3686	516	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280615.1	s__Chryseoglobus sp002280615	81.3077	276	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502445.1	s__Yonghaparkia sp005502445	81.2285	414	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200395.1	s__Chryseoglobus frigidaquae	81.1001	467	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009371975.2	s__Marinisubtilis pacificus	80.7297	446	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	97.81	97.81	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-03-16 03:25:02,295] [INFO] GTDB search result was written to OceanDNA-b2665/result_gtdb.tsv
[2023-03-16 03:25:02,295] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:25:02,297] [INFO] DFAST_QC result json was written to OceanDNA-b2665/dqc_result.json
[2023-03-16 03:25:02,297] [INFO] DFAST_QC completed!
[2023-03-16 03:25:02,297] [INFO] Total running time: 0h1m14s