[2023-06-19 04:44:26,625] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:44:26,627] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:44:26,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c9312fd-4c0b-4d9b-97de-37b26f06164d/dqc_reference
[2023-06-19 04:44:28,147] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:44:28,148] [INFO] Task started: Prodigal
[2023-06-19 04:44:28,148] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a6e7550-2e00-45d1-b828-5f9bd1795674/GCA_018052955.1_ASM1805295v1_genomic.fna.gz | prodigal -d GCA_018052955.1_ASM1805295v1_genomic.fna/cds.fna -a GCA_018052955.1_ASM1805295v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:44:29,992] [INFO] Task succeeded: Prodigal
[2023-06-19 04:44:29,993] [INFO] Task started: HMMsearch
[2023-06-19 04:44:29,993] [INFO] Running command: hmmsearch --tblout GCA_018052955.1_ASM1805295v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c9312fd-4c0b-4d9b-97de-37b26f06164d/dqc_reference/reference_markers.hmm GCA_018052955.1_ASM1805295v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:44:30,308] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:44:30,310] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4a6e7550-2e00-45d1-b828-5f9bd1795674/GCA_018052955.1_ASM1805295v1_genomic.fna.gz]
[2023-06-19 04:44:30,353] [INFO] Query marker FASTA was written to GCA_018052955.1_ASM1805295v1_genomic.fna/markers.fasta
[2023-06-19 04:44:30,353] [INFO] Task started: Blastn
[2023-06-19 04:44:30,353] [INFO] Running command: blastn -query GCA_018052955.1_ASM1805295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9312fd-4c0b-4d9b-97de-37b26f06164d/dqc_reference/reference_markers.fasta -out GCA_018052955.1_ASM1805295v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:44:30,959] [INFO] Task succeeded: Blastn
[2023-06-19 04:44:31,039] [INFO] Selected 15 target genomes.
[2023-06-19 04:44:31,040] [INFO] Target genome list was writen to GCA_018052955.1_ASM1805295v1_genomic.fna/target_genomes.txt
[2023-06-19 04:44:31,044] [INFO] Task started: fastANI
[2023-06-19 04:44:31,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6e7550-2e00-45d1-b828-5f9bd1795674/GCA_018052955.1_ASM1805295v1_genomic.fna.gz --refList GCA_018052955.1_ASM1805295v1_genomic.fna/target_genomes.txt --output GCA_018052955.1_ASM1805295v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:44:38,482] [INFO] Task succeeded: fastANI
[2023-06-19 04:44:38,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c9312fd-4c0b-4d9b-97de-37b26f06164d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:44:38,483] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c9312fd-4c0b-4d9b-97de-37b26f06164d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:44:38,490] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:44:38,490] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:44:38,490] [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 04:44:38,492] [INFO] DFAST Taxonomy check result was written to GCA_018052955.1_ASM1805295v1_genomic.fna/tc_result.tsv
[2023-06-19 04:44:38,493] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:44:38,493] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:44:38,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c9312fd-4c0b-4d9b-97de-37b26f06164d/dqc_reference/checkm_data
[2023-06-19 04:44:38,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:44:38,519] [INFO] Task started: CheckM
[2023-06-19 04:44:38,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018052955.1_ASM1805295v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018052955.1_ASM1805295v1_genomic.fna/checkm_input GCA_018052955.1_ASM1805295v1_genomic.fna/checkm_result
[2023-06-19 04:44:52,778] [INFO] Task succeeded: CheckM
[2023-06-19 04:44:52,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 04:44:52,840] [INFO] ===== Completeness check finished =====
[2023-06-19 04:44:52,841] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:44:52,841] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018052955.1_ASM1805295v1_genomic.fna/markers.fasta)
[2023-06-19 04:44:52,841] [INFO] Task started: Blastn
[2023-06-19 04:44:52,842] [INFO] Running command: blastn -query GCA_018052955.1_ASM1805295v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c9312fd-4c0b-4d9b-97de-37b26f06164d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018052955.1_ASM1805295v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:44:53,427] [INFO] Task succeeded: Blastn
[2023-06-19 04:44:53,435] [INFO] Selected 12 target genomes.
[2023-06-19 04:44:53,436] [INFO] Target genome list was writen to GCA_018052955.1_ASM1805295v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:44:53,448] [INFO] Task started: fastANI
[2023-06-19 04:44:53,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6e7550-2e00-45d1-b828-5f9bd1795674/GCA_018052955.1_ASM1805295v1_genomic.fna.gz --refList GCA_018052955.1_ASM1805295v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018052955.1_ASM1805295v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:44:58,107] [INFO] Task succeeded: fastANI
[2023-06-19 04:44:58,123] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:44:58,123] [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_000431335.1	s__CAG-269 sp000431335	99.5284	321	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.17	98.64	0.90	0.86	6	conclusive
GCA_900556945.1	s__CAG-269 sp900556945	82.4648	154	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.30	99.23	0.81	0.81	3	-
GCA_900556695.1	s__CAG-269 sp900556695	80.9973	161	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554565.1	s__CAG-269 sp900554565	80.9004	221	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.93	97.94	0.90	0.85	3	-
GCA_905213875.1	s__CAG-269 sp905213875	80.8925	218	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.16	98.07	0.72	0.64	3	-
GCA_900762425.1	s__CAG-269 sp900762425	80.3624	213	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014846485.1	s__CAG-269 sp014846485	80.1857	198	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554365.1	s__CAG-269 sp900554365	80.0745	196	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905215845.1	s__CAG-269 sp905215845	80.0518	124	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001916005.1	s__CAG-269 sp001916005	79.4803	193	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	96.70	96.22	0.72	0.66	3	-
GCA_000437215.1	s__CAG-269 sp000437215	79.3696	191	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.98	98.94	0.85	0.85	3	-
GCA_904419495.1	s__CAG-269 sp904419495	79.3386	190	343	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:44:58,127] [INFO] GTDB search result was written to GCA_018052955.1_ASM1805295v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:44:58,128] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:44:58,135] [INFO] DFAST_QC result json was written to GCA_018052955.1_ASM1805295v1_genomic.fna/dqc_result.json
[2023-06-19 04:44:58,135] [INFO] DFAST_QC completed!
[2023-06-19 04:44:58,135] [INFO] Total running time: 0h0m32s