[2023-06-18 23:43:44,078] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:43:44,080] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:43:44,080] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d583e4b-1a64-45a7-942e-7c9624ee4d01/dqc_reference
[2023-06-18 23:43:45,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:43:45,408] [INFO] Task started: Prodigal
[2023-06-18 23:43:45,410] [INFO] Running command: gunzip -c /var/lib/cwl/stge5bbd395-236e-4aa6-a14a-660cd061f0d2/GCA_018059645.1_ASM1805964v1_genomic.fna.gz | prodigal -d GCA_018059645.1_ASM1805964v1_genomic.fna/cds.fna -a GCA_018059645.1_ASM1805964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:43:51,456] [INFO] Task succeeded: Prodigal
[2023-06-18 23:43:51,457] [INFO] Task started: HMMsearch
[2023-06-18 23:43:51,457] [INFO] Running command: hmmsearch --tblout GCA_018059645.1_ASM1805964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d583e4b-1a64-45a7-942e-7c9624ee4d01/dqc_reference/reference_markers.hmm GCA_018059645.1_ASM1805964v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:43:51,707] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:43:51,709] [INFO] Found 6/6 markers.
[2023-06-18 23:43:51,736] [INFO] Query marker FASTA was written to GCA_018059645.1_ASM1805964v1_genomic.fna/markers.fasta
[2023-06-18 23:43:51,737] [INFO] Task started: Blastn
[2023-06-18 23:43:51,737] [INFO] Running command: blastn -query GCA_018059645.1_ASM1805964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d583e4b-1a64-45a7-942e-7c9624ee4d01/dqc_reference/reference_markers.fasta -out GCA_018059645.1_ASM1805964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:52,389] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:52,393] [INFO] Selected 26 target genomes.
[2023-06-18 23:43:52,393] [INFO] Target genome list was writen to GCA_018059645.1_ASM1805964v1_genomic.fna/target_genomes.txt
[2023-06-18 23:43:52,398] [INFO] Task started: fastANI
[2023-06-18 23:43:52,399] [INFO] Running command: fastANI --query /var/lib/cwl/stge5bbd395-236e-4aa6-a14a-660cd061f0d2/GCA_018059645.1_ASM1805964v1_genomic.fna.gz --refList GCA_018059645.1_ASM1805964v1_genomic.fna/target_genomes.txt --output GCA_018059645.1_ASM1805964v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:44:07,874] [INFO] Task succeeded: fastANI
[2023-06-18 23:44:07,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d583e4b-1a64-45a7-942e-7c9624ee4d01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:44:07,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d583e4b-1a64-45a7-942e-7c9624ee4d01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:44:07,878] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:44:07,878] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 23:44:07,878] [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
--------------------------------------------------------------------------------
[2023-06-18 23:44:07,880] [INFO] DFAST Taxonomy check result was written to GCA_018059645.1_ASM1805964v1_genomic.fna/tc_result.tsv
[2023-06-18 23:44:07,881] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:44:07,881] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:44:07,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d583e4b-1a64-45a7-942e-7c9624ee4d01/dqc_reference/checkm_data
[2023-06-18 23:44:07,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:44:07,911] [INFO] Task started: CheckM
[2023-06-18 23:44:07,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018059645.1_ASM1805964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018059645.1_ASM1805964v1_genomic.fna/checkm_input GCA_018059645.1_ASM1805964v1_genomic.fna/checkm_result
[2023-06-18 23:44:31,057] [INFO] Task succeeded: CheckM
[2023-06-18 23:44:31,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 23:44:31,076] [INFO] ===== Completeness check finished =====
[2023-06-18 23:44:31,076] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:44:31,077] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018059645.1_ASM1805964v1_genomic.fna/markers.fasta)
[2023-06-18 23:44:31,077] [INFO] Task started: Blastn
[2023-06-18 23:44:31,078] [INFO] Running command: blastn -query GCA_018059645.1_ASM1805964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d583e4b-1a64-45a7-942e-7c9624ee4d01/dqc_reference/reference_markers_gtdb.fasta -out GCA_018059645.1_ASM1805964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:44:32,210] [INFO] Task succeeded: Blastn
[2023-06-18 23:44:32,215] [INFO] Selected 15 target genomes.
[2023-06-18 23:44:32,215] [INFO] Target genome list was writen to GCA_018059645.1_ASM1805964v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:44:32,224] [INFO] Task started: fastANI
[2023-06-18 23:44:32,225] [INFO] Running command: fastANI --query /var/lib/cwl/stge5bbd395-236e-4aa6-a14a-660cd061f0d2/GCA_018059645.1_ASM1805964v1_genomic.fna.gz --refList GCA_018059645.1_ASM1805964v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018059645.1_ASM1805964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:44:39,798] [INFO] Task succeeded: fastANI
[2023-06-18 23:44:39,811] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:44:39,811] [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_002071335.1	s__Lenti-01 sp002071335	98.2342	429	549	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__Lenti-01	95.0	98.24	98.18	0.77	0.75	3	conclusive
GCA_002347655.1	s__Lenti-01 sp002347655	78.6857	235	549	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__Lenti-01	95.0	99.93	99.93	0.97	0.97	2	-
GCA_009930415.1	s__Lenti-01 sp009930415	78.4504	208	549	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__Lenti-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009928955.1	s__Lenti-01 sp009928955	78.3253	197	549	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__Lenti-01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012511885.1	s__JAAZFE01 sp012511885	78.2231	153	549	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__JAAZFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432565.1	s__JAAZFE01 sp018432565	77.9993	137	549	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__JAAZFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514035.1	s__Lenti-01 sp012514035	77.9498	187	549	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__Lenti-01	95.0	99.67	99.67	0.89	0.89	2	-
GCA_002304915.1	s__Lenti-01 sp002304915	77.817	165	549	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__Lenti-01	95.0	98.98	98.51	0.80	0.79	4	-
GCA_003451935.1	s__Lenti-01 sp003451935	77.6125	129	549	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__LD1-PB3;f__Lenti-01;g__Lenti-01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 23:44:39,814] [INFO] GTDB search result was written to GCA_018059645.1_ASM1805964v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:44:39,815] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:44:39,818] [INFO] DFAST_QC result json was written to GCA_018059645.1_ASM1805964v1_genomic.fna/dqc_result.json
[2023-06-18 23:44:39,818] [INFO] DFAST_QC completed!
[2023-06-18 23:44:39,818] [INFO] Total running time: 0h0m56s