[2023-06-19 01:08:59,367] [INFO] DFAST_QC pipeline started.
[2023-06-19 01:08:59,369] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 01:08:59,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg03d1dc1c-39a2-45f8-9215-35dc2141777a/dqc_reference
[2023-06-19 01:09:00,676] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 01:09:00,679] [INFO] Task started: Prodigal
[2023-06-19 01:09:00,680] [INFO] Running command: gunzip -c /var/lib/cwl/stgd342a472-1cf4-4583-9fbb-6316adf989f5/GCA_018970925.1_ASM1897092v1_genomic.fna.gz | prodigal -d GCA_018970925.1_ASM1897092v1_genomic.fna/cds.fna -a GCA_018970925.1_ASM1897092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 01:09:02,177] [INFO] Task succeeded: Prodigal
[2023-06-19 01:09:02,178] [INFO] Task started: HMMsearch
[2023-06-19 01:09:02,178] [INFO] Running command: hmmsearch --tblout GCA_018970925.1_ASM1897092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03d1dc1c-39a2-45f8-9215-35dc2141777a/dqc_reference/reference_markers.hmm GCA_018970925.1_ASM1897092v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 01:09:02,381] [INFO] Task succeeded: HMMsearch
[2023-06-19 01:09:02,382] [INFO] Found 6/6 markers.
[2023-06-19 01:09:02,400] [INFO] Query marker FASTA was written to GCA_018970925.1_ASM1897092v1_genomic.fna/markers.fasta
[2023-06-19 01:09:02,400] [INFO] Task started: Blastn
[2023-06-19 01:09:02,400] [INFO] Running command: blastn -query GCA_018970925.1_ASM1897092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03d1dc1c-39a2-45f8-9215-35dc2141777a/dqc_reference/reference_markers.fasta -out GCA_018970925.1_ASM1897092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:09:04,987] [INFO] Task succeeded: Blastn
[2023-06-19 01:09:04,993] [INFO] Selected 17 target genomes.
[2023-06-19 01:09:04,994] [INFO] Target genome list was writen to GCA_018970925.1_ASM1897092v1_genomic.fna/target_genomes.txt
[2023-06-19 01:09:04,997] [INFO] Task started: fastANI
[2023-06-19 01:09:04,997] [INFO] Running command: fastANI --query /var/lib/cwl/stgd342a472-1cf4-4583-9fbb-6316adf989f5/GCA_018970925.1_ASM1897092v1_genomic.fna.gz --refList GCA_018970925.1_ASM1897092v1_genomic.fna/target_genomes.txt --output GCA_018970925.1_ASM1897092v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 01:09:13,130] [INFO] Task succeeded: fastANI
[2023-06-19 01:09:13,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03d1dc1c-39a2-45f8-9215-35dc2141777a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 01:09:13,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03d1dc1c-39a2-45f8-9215-35dc2141777a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 01:09:13,133] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 01:09:13,133] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 01:09:13,133] [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
--------------------------------------------------------------------------------
[2023-06-19 01:09:13,134] [INFO] DFAST Taxonomy check result was written to GCA_018970925.1_ASM1897092v1_genomic.fna/tc_result.tsv
[2023-06-19 01:09:13,135] [INFO] ===== Taxonomy check completed =====
[2023-06-19 01:09:13,135] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 01:09:13,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03d1dc1c-39a2-45f8-9215-35dc2141777a/dqc_reference/checkm_data
[2023-06-19 01:09:13,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 01:09:13,150] [INFO] Task started: CheckM
[2023-06-19 01:09:13,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018970925.1_ASM1897092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018970925.1_ASM1897092v1_genomic.fna/checkm_input GCA_018970925.1_ASM1897092v1_genomic.fna/checkm_result
[2023-06-19 01:09:25,608] [INFO] Task succeeded: CheckM
[2023-06-19 01:09:25,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.51%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 01:09:25,630] [INFO] ===== Completeness check finished =====
[2023-06-19 01:09:25,630] [INFO] ===== Start GTDB Search =====
[2023-06-19 01:09:25,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018970925.1_ASM1897092v1_genomic.fna/markers.fasta)
[2023-06-19 01:09:25,631] [INFO] Task started: Blastn
[2023-06-19 01:09:25,631] [INFO] Running command: blastn -query GCA_018970925.1_ASM1897092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03d1dc1c-39a2-45f8-9215-35dc2141777a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018970925.1_ASM1897092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 01:09:26,416] [INFO] Task succeeded: Blastn
[2023-06-19 01:09:26,424] [INFO] Selected 7 target genomes.
[2023-06-19 01:09:26,424] [INFO] Target genome list was writen to GCA_018970925.1_ASM1897092v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 01:09:26,431] [INFO] Task started: fastANI
[2023-06-19 01:09:26,432] [INFO] Running command: fastANI --query /var/lib/cwl/stgd342a472-1cf4-4583-9fbb-6316adf989f5/GCA_018970925.1_ASM1897092v1_genomic.fna.gz --refList GCA_018970925.1_ASM1897092v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018970925.1_ASM1897092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 01:09:27,787] [INFO] Task succeeded: fastANI
[2023-06-19 01:09:27,796] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 01:09:27,796] [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
GCA_003569145.1	s__MAG-120802 sp003569145	97.0971	158	177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	99.02	99.02	0.96	0.96	2	conclusive
GCA_016870795.1	s__MAG-120802 sp016870795	93.9475	149	177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777515.1	s__MAG-120802 sp005777515	92.7944	122	177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	98.53	98.39	0.77	0.76	3	-
GCA_002347935.1	s__MAG-120802 sp002347935	87.8867	129	177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	98.96	98.66	0.86	0.80	28	-
GCA_016870365.1	s__MAG-120802 sp016870365	80.8159	132	177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882885.1	s__MAG-120802 sp018882885	77.5097	58	177	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__MAG-120802	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 01:09:27,797] [INFO] GTDB search result was written to GCA_018970925.1_ASM1897092v1_genomic.fna/result_gtdb.tsv
[2023-06-19 01:09:27,798] [INFO] ===== GTDB Search completed =====
[2023-06-19 01:09:27,802] [INFO] DFAST_QC result json was written to GCA_018970925.1_ASM1897092v1_genomic.fna/dqc_result.json
[2023-06-19 01:09:27,802] [INFO] DFAST_QC completed!
[2023-06-19 01:09:27,802] [INFO] Total running time: 0h0m28s