[2023-06-26 23:52:21,318] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:52:21,322] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:52:21,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e3996b9-3e23-445b-b08f-5e808875371b/dqc_reference
[2023-06-26 23:52:22,584] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:52:22,585] [INFO] Task started: Prodigal
[2023-06-26 23:52:22,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg4459f363-cd2b-4574-bebe-72fc68248933/GCA_026708115.1_ASM2670811v1_genomic.fna.gz | prodigal -d GCA_026708115.1_ASM2670811v1_genomic.fna/cds.fna -a GCA_026708115.1_ASM2670811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:52:36,914] [INFO] Task succeeded: Prodigal
[2023-06-26 23:52:36,915] [INFO] Task started: HMMsearch
[2023-06-26 23:52:36,915] [INFO] Running command: hmmsearch --tblout GCA_026708115.1_ASM2670811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e3996b9-3e23-445b-b08f-5e808875371b/dqc_reference/reference_markers.hmm GCA_026708115.1_ASM2670811v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:52:37,209] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:52:37,210] [INFO] Found 6/6 markers.
[2023-06-26 23:52:37,252] [INFO] Query marker FASTA was written to GCA_026708115.1_ASM2670811v1_genomic.fna/markers.fasta
[2023-06-26 23:52:37,252] [INFO] Task started: Blastn
[2023-06-26 23:52:37,253] [INFO] Running command: blastn -query GCA_026708115.1_ASM2670811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e3996b9-3e23-445b-b08f-5e808875371b/dqc_reference/reference_markers.fasta -out GCA_026708115.1_ASM2670811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:52:37,839] [INFO] Task succeeded: Blastn
[2023-06-26 23:52:37,843] [INFO] Selected 20 target genomes.
[2023-06-26 23:52:37,843] [INFO] Target genome list was writen to GCA_026708115.1_ASM2670811v1_genomic.fna/target_genomes.txt
[2023-06-26 23:52:37,852] [INFO] Task started: fastANI
[2023-06-26 23:52:37,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg4459f363-cd2b-4574-bebe-72fc68248933/GCA_026708115.1_ASM2670811v1_genomic.fna.gz --refList GCA_026708115.1_ASM2670811v1_genomic.fna/target_genomes.txt --output GCA_026708115.1_ASM2670811v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:52:52,570] [INFO] Task succeeded: fastANI
[2023-06-26 23:52:52,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e3996b9-3e23-445b-b08f-5e808875371b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:52:52,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e3996b9-3e23-445b-b08f-5e808875371b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:52:52,589] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:52:52,589] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-26 23:52:52,589] [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
--------------------------------------------------------------------------------
[2023-06-26 23:52:52,592] [INFO] DFAST Taxonomy check result was written to GCA_026708115.1_ASM2670811v1_genomic.fna/tc_result.tsv
[2023-06-26 23:52:52,593] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:52:52,593] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:52:52,593] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e3996b9-3e23-445b-b08f-5e808875371b/dqc_reference/checkm_data
[2023-06-26 23:52:52,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:52:52,645] [INFO] Task started: CheckM
[2023-06-26 23:52:52,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708115.1_ASM2670811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708115.1_ASM2670811v1_genomic.fna/checkm_input GCA_026708115.1_ASM2670811v1_genomic.fna/checkm_result
[2023-06-26 23:53:36,152] [INFO] Task succeeded: CheckM
[2023-06-26 23:53:36,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:53:36,180] [INFO] ===== Completeness check finished =====
[2023-06-26 23:53:36,180] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:53:36,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708115.1_ASM2670811v1_genomic.fna/markers.fasta)
[2023-06-26 23:53:36,181] [INFO] Task started: Blastn
[2023-06-26 23:53:36,181] [INFO] Running command: blastn -query GCA_026708115.1_ASM2670811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e3996b9-3e23-445b-b08f-5e808875371b/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708115.1_ASM2670811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:53:36,961] [INFO] Task succeeded: Blastn
[2023-06-26 23:53:36,965] [INFO] Selected 22 target genomes.
[2023-06-26 23:53:36,966] [INFO] Target genome list was writen to GCA_026708115.1_ASM2670811v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:53:36,984] [INFO] Task started: fastANI
[2023-06-26 23:53:36,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg4459f363-cd2b-4574-bebe-72fc68248933/GCA_026708115.1_ASM2670811v1_genomic.fna.gz --refList GCA_026708115.1_ASM2670811v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708115.1_ASM2670811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:53:52,945] [INFO] Task succeeded: fastANI
[2023-06-26 23:53:52,959] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:53:52,960] [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_011525385.1	s__UBA6055 sp011525385	90.1074	1367	1583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523545.1	s__UBA6055 sp011523545	78.8007	556	1583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270545.1	s__UBA6055 sp012270545	78.7407	488	1583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523705.1	s__UBA6055 sp011523705	78.5227	524	1583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523515.1	s__UBA6055 sp011523515	78.2809	480	1583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841405.1	s__UBA6055 sp009841405	77.8092	476	1583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238485.1	s__UBA6055 sp002238485	77.5869	335	1583	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__UBA6055	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:53:52,962] [INFO] GTDB search result was written to GCA_026708115.1_ASM2670811v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:53:52,963] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:53:52,967] [INFO] DFAST_QC result json was written to GCA_026708115.1_ASM2670811v1_genomic.fna/dqc_result.json
[2023-06-26 23:53:52,967] [INFO] DFAST_QC completed!
[2023-06-26 23:53:52,967] [INFO] Total running time: 0h1m32s