[2023-06-27 17:41:17,345] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:41:17,350] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:41:17,351] [INFO] DQC Reference Directory: /var/lib/cwl/stge1084168-5aa6-43f5-9e99-82bdb8843187/dqc_reference
[2023-06-27 17:41:18,646] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:41:18,647] [INFO] Task started: Prodigal
[2023-06-27 17:41:18,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f5cc151-eb11-43a9-a321-4fb83b14680a/GCA_002503545.1_ASM250354v1_genomic.fna.gz | prodigal -d GCA_002503545.1_ASM250354v1_genomic.fna/cds.fna -a GCA_002503545.1_ASM250354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:41:26,147] [INFO] Task succeeded: Prodigal
[2023-06-27 17:41:26,147] [INFO] Task started: HMMsearch
[2023-06-27 17:41:26,147] [INFO] Running command: hmmsearch --tblout GCA_002503545.1_ASM250354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1084168-5aa6-43f5-9e99-82bdb8843187/dqc_reference/reference_markers.hmm GCA_002503545.1_ASM250354v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:41:26,379] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:41:26,381] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9f5cc151-eb11-43a9-a321-4fb83b14680a/GCA_002503545.1_ASM250354v1_genomic.fna.gz]
[2023-06-27 17:41:26,396] [INFO] Query marker FASTA was written to GCA_002503545.1_ASM250354v1_genomic.fna/markers.fasta
[2023-06-27 17:41:26,397] [INFO] Task started: Blastn
[2023-06-27 17:41:26,397] [INFO] Running command: blastn -query GCA_002503545.1_ASM250354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1084168-5aa6-43f5-9e99-82bdb8843187/dqc_reference/reference_markers.fasta -out GCA_002503545.1_ASM250354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:26,873] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:26,877] [INFO] Selected 10 target genomes.
[2023-06-27 17:41:26,877] [INFO] Target genome list was writen to GCA_002503545.1_ASM250354v1_genomic.fna/target_genomes.txt
[2023-06-27 17:41:26,882] [INFO] Task started: fastANI
[2023-06-27 17:41:26,883] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5cc151-eb11-43a9-a321-4fb83b14680a/GCA_002503545.1_ASM250354v1_genomic.fna.gz --refList GCA_002503545.1_ASM250354v1_genomic.fna/target_genomes.txt --output GCA_002503545.1_ASM250354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:41:33,236] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:33,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1084168-5aa6-43f5-9e99-82bdb8843187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:41:33,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1084168-5aa6-43f5-9e99-82bdb8843187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:41:33,238] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 17:41:33,238] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 17:41:33,238] [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
--------------------------------------------------------------------------------
[2023-06-27 17:41:33,240] [INFO] DFAST Taxonomy check result was written to GCA_002503545.1_ASM250354v1_genomic.fna/tc_result.tsv
[2023-06-27 17:41:33,241] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:41:33,241] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:41:33,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1084168-5aa6-43f5-9e99-82bdb8843187/dqc_reference/checkm_data
[2023-06-27 17:41:33,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:41:33,262] [INFO] Task started: CheckM
[2023-06-27 17:41:33,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002503545.1_ASM250354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002503545.1_ASM250354v1_genomic.fna/checkm_input GCA_002503545.1_ASM250354v1_genomic.fna/checkm_result
[2023-06-27 17:41:59,640] [INFO] Task succeeded: CheckM
[2023-06-27 17:41:59,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.87%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 17:41:59,664] [INFO] ===== Completeness check finished =====
[2023-06-27 17:41:59,664] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:41:59,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002503545.1_ASM250354v1_genomic.fna/markers.fasta)
[2023-06-27 17:41:59,665] [INFO] Task started: Blastn
[2023-06-27 17:41:59,665] [INFO] Running command: blastn -query GCA_002503545.1_ASM250354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1084168-5aa6-43f5-9e99-82bdb8843187/dqc_reference/reference_markers_gtdb.fasta -out GCA_002503545.1_ASM250354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:42:00,158] [INFO] Task succeeded: Blastn
[2023-06-27 17:42:00,162] [INFO] Selected 10 target genomes.
[2023-06-27 17:42:00,163] [INFO] Target genome list was writen to GCA_002503545.1_ASM250354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:42:00,169] [INFO] Task started: fastANI
[2023-06-27 17:42:00,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f5cc151-eb11-43a9-a321-4fb83b14680a/GCA_002503545.1_ASM250354v1_genomic.fna.gz --refList GCA_002503545.1_ASM250354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002503545.1_ASM250354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:42:03,364] [INFO] Task succeeded: fastANI
[2023-06-27 17:42:03,374] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 17:42:03,375] [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_002503545.1	s__Methanomethylophilus sp002503545	100.0	397	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000300255.2	s__Methanomethylophilus alvus	83.075	317	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	99.45	99.02	0.97	0.92	6	-
GCA_902787415.1	s__Methanomethylophilus sp902787415	79.8996	163	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	97.47	96.90	0.79	0.76	3	-
GCA_001560915.1	s__Methanomethylophilus sp001560915	79.1322	148	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	96.94	96.83	0.93	0.92	3	-
GCA_902763685.1	s__Methanomethylophilus sp902763685	78.8663	158	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015063225.1	s__Methanomethylophilus sp015063225	78.8097	147	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__Methanomethylophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009911715.1	s__UBA71 sp006954425	78.292	134	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	96.86	96.86	0.82	0.82	2	-
GCA_017519045.1	s__UBA71 sp017519045	77.7793	95	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	98.48	98.48	0.77	0.77	2	-
GCA_017540825.1	s__UBA71 sp017540825	77.4671	108	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__UBA71	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515075.1	s__JAAYZC01 sp012515075	76.8662	62	401	d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__JAAYZC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 17:42:03,377] [INFO] GTDB search result was written to GCA_002503545.1_ASM250354v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:42:03,377] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:42:03,382] [INFO] DFAST_QC result json was written to GCA_002503545.1_ASM250354v1_genomic.fna/dqc_result.json
[2023-06-27 17:42:03,383] [INFO] DFAST_QC completed!
[2023-06-27 17:42:03,383] [INFO] Total running time: 0h0m46s