[2023-03-18 20:55:47,284] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:55:47,284] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:55:47,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg744c9379-d389-4d45-a9be-13fab6c32c8a/dqc_reference
[2023-03-18 20:55:48,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:55:48,399] [INFO] Task started: Prodigal
[2023-03-18 20:55:48,400] [INFO] Running command: cat /var/lib/cwl/stg5484b57c-a150-4ec3-aae0-0b9ffe4c75b1/OceanDNA-b2821.fa | prodigal -d OceanDNA-b2821/cds.fna -a OceanDNA-b2821/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:55:57,720] [INFO] Task succeeded: Prodigal
[2023-03-18 20:55:57,720] [INFO] Task started: HMMsearch
[2023-03-18 20:55:57,720] [INFO] Running command: hmmsearch --tblout OceanDNA-b2821/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg744c9379-d389-4d45-a9be-13fab6c32c8a/dqc_reference/reference_markers.hmm OceanDNA-b2821/protein.faa > /dev/null
[2023-03-18 20:55:57,873] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:55:57,873] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5484b57c-a150-4ec3-aae0-0b9ffe4c75b1/OceanDNA-b2821.fa]
[2023-03-18 20:55:57,888] [INFO] Query marker FASTA was written to OceanDNA-b2821/markers.fasta
[2023-03-18 20:55:57,888] [INFO] Task started: Blastn
[2023-03-18 20:55:57,888] [INFO] Running command: blastn -query OceanDNA-b2821/markers.fasta -db /var/lib/cwl/stg744c9379-d389-4d45-a9be-13fab6c32c8a/dqc_reference/reference_markers.fasta -out OceanDNA-b2821/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:55:58,759] [INFO] Task succeeded: Blastn
[2023-03-18 20:55:58,760] [INFO] Selected 15 target genomes.
[2023-03-18 20:55:58,760] [INFO] Target genome list was writen to OceanDNA-b2821/target_genomes.txt
[2023-03-18 20:55:58,768] [INFO] Task started: fastANI
[2023-03-18 20:55:58,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg5484b57c-a150-4ec3-aae0-0b9ffe4c75b1/OceanDNA-b2821.fa --refList OceanDNA-b2821/target_genomes.txt --output OceanDNA-b2821/fastani_result.tsv --threads 1
[2023-03-18 20:56:06,692] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:06,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg744c9379-d389-4d45-a9be-13fab6c32c8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:56:06,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg744c9379-d389-4d45-a9be-13fab6c32c8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:56:06,702] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:56:06,702] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:56:06,702] [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
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	82.389	336	482	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	82.3074	338	482	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	80.7395	285	482	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	80.7374	292	482	95	below_threshold
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	80.505	286	482	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.5747	272	482	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.3545	252	482	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	79.0976	217	482	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.0605	239	482	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.969	222	482	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	78.8164	229	482	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	78.7264	229	482	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	78.6915	218	482	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	78.64	229	482	95	below_threshold
Marisediminicola senii	strain=SM7_A14	GCA_011057645.1	2711233	2711233	type	True	78.5911	218	482	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:56:06,702] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2821/tc_result.tsv
[2023-03-18 20:56:06,702] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:56:06,702] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:56:06,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg744c9379-d389-4d45-a9be-13fab6c32c8a/dqc_reference/checkm_data
[2023-03-18 20:56:06,703] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:56:06,706] [INFO] Task started: CheckM
[2023-03-18 20:56:06,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2821/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2821/checkm_input OceanDNA-b2821/checkm_result
[2023-03-18 20:56:34,031] [INFO] Task succeeded: CheckM
[2023-03-18 20:56:34,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.06%
Contamintation: 0.76%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 20:56:34,033] [INFO] ===== Completeness check finished =====
[2023-03-18 20:56:34,034] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:56:34,034] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2821/markers.fasta)
[2023-03-18 20:56:34,034] [INFO] Task started: Blastn
[2023-03-18 20:56:34,034] [INFO] Running command: blastn -query OceanDNA-b2821/markers.fasta -db /var/lib/cwl/stg744c9379-d389-4d45-a9be-13fab6c32c8a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2821/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:35,307] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:35,308] [INFO] Selected 9 target genomes.
[2023-03-18 20:56:35,308] [INFO] Target genome list was writen to OceanDNA-b2821/target_genomes_gtdb.txt
[2023-03-18 20:56:35,388] [INFO] Task started: fastANI
[2023-03-18 20:56:35,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg5484b57c-a150-4ec3-aae0-0b9ffe4c75b1/OceanDNA-b2821.fa --refList OceanDNA-b2821/target_genomes_gtdb.txt --output OceanDNA-b2821/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:56:39,800] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:39,806] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 20:56:39,806] [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_009371975.2	s__Marinisubtilis pacificus	97.57	444	482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	97.81	97.81	0.83	0.83	2	conclusive
GCF_013414345.1	s__Marinisubtilis indicus	93.2821	426	482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
GCF_002813345.1	s__Marinisubtilis sp002813345	84.7943	367	482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464255.1	s__Chryseoglobus sp001464255	82.8716	275	482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280615.1	s__Chryseoglobus sp002280615	82.8598	235	482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425665.1	s__Yonghaparkia sp001425665	82.4711	334	482	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	82.4445	339	482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	82.2793	338	482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_005502445.1	s__Yonghaparkia sp005502445	81.9999	321	482	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:56:39,806] [INFO] GTDB search result was written to OceanDNA-b2821/result_gtdb.tsv
[2023-03-18 20:56:39,806] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:56:39,808] [INFO] DFAST_QC result json was written to OceanDNA-b2821/dqc_result.json
[2023-03-18 20:56:39,808] [INFO] DFAST_QC completed!
[2023-03-18 20:56:39,808] [INFO] Total running time: 0h0m53s