[2023-06-04 22:52:22,768] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:52:22,776] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:52:22,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg39a0572b-c389-4633-a4bb-c9505223bbbf/dqc_reference
[2023-06-04 22:52:24,329] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:52:24,329] [INFO] Task started: Prodigal
[2023-06-04 22:52:24,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg59bf7822-06e6-470f-9052-47b6a44cd8fe/GCA_934167455.1_ERR7738551_bin.11_genomic.fna.gz | prodigal -d GCA_934167455.1_ERR7738551_bin.11_genomic.fna/cds.fna -a GCA_934167455.1_ERR7738551_bin.11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:52:26,546] [INFO] Task succeeded: Prodigal
[2023-06-04 22:52:26,546] [INFO] Task started: HMMsearch
[2023-06-04 22:52:26,546] [INFO] Running command: hmmsearch --tblout GCA_934167455.1_ERR7738551_bin.11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39a0572b-c389-4633-a4bb-c9505223bbbf/dqc_reference/reference_markers.hmm GCA_934167455.1_ERR7738551_bin.11_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:52:26,785] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:52:26,786] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg59bf7822-06e6-470f-9052-47b6a44cd8fe/GCA_934167455.1_ERR7738551_bin.11_genomic.fna.gz]
[2023-06-04 22:52:26,803] [INFO] Query marker FASTA was written to GCA_934167455.1_ERR7738551_bin.11_genomic.fna/markers.fasta
[2023-06-04 22:52:26,804] [INFO] Task started: Blastn
[2023-06-04 22:52:26,804] [INFO] Running command: blastn -query GCA_934167455.1_ERR7738551_bin.11_genomic.fna/markers.fasta -db /var/lib/cwl/stg39a0572b-c389-4633-a4bb-c9505223bbbf/dqc_reference/reference_markers.fasta -out GCA_934167455.1_ERR7738551_bin.11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:52:27,389] [INFO] Task succeeded: Blastn
[2023-06-04 22:52:27,403] [INFO] Selected 21 target genomes.
[2023-06-04 22:52:27,404] [INFO] Target genome list was writen to GCA_934167455.1_ERR7738551_bin.11_genomic.fna/target_genomes.txt
[2023-06-04 22:52:27,409] [INFO] Task started: fastANI
[2023-06-04 22:52:27,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg59bf7822-06e6-470f-9052-47b6a44cd8fe/GCA_934167455.1_ERR7738551_bin.11_genomic.fna.gz --refList GCA_934167455.1_ERR7738551_bin.11_genomic.fna/target_genomes.txt --output GCA_934167455.1_ERR7738551_bin.11_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:52:36,188] [INFO] Task succeeded: fastANI
[2023-06-04 22:52:36,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39a0572b-c389-4633-a4bb-c9505223bbbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:52:36,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39a0572b-c389-4633-a4bb-c9505223bbbf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:52:36,190] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:52:36,190] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 22:52:36,190] [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
--------------------------------------------------------------------------------
[2023-06-04 22:52:36,193] [INFO] DFAST Taxonomy check result was written to GCA_934167455.1_ERR7738551_bin.11_genomic.fna/tc_result.tsv
[2023-06-04 22:52:36,193] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:52:36,193] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:52:36,194] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39a0572b-c389-4633-a4bb-c9505223bbbf/dqc_reference/checkm_data
[2023-06-04 22:52:36,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:52:36,219] [INFO] Task started: CheckM
[2023-06-04 22:52:36,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934167455.1_ERR7738551_bin.11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934167455.1_ERR7738551_bin.11_genomic.fna/checkm_input GCA_934167455.1_ERR7738551_bin.11_genomic.fna/checkm_result
[2023-06-04 22:52:51,389] [INFO] Task succeeded: CheckM
[2023-06-04 22:52:51,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:52:51,410] [INFO] ===== Completeness check finished =====
[2023-06-04 22:52:51,410] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:52:51,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934167455.1_ERR7738551_bin.11_genomic.fna/markers.fasta)
[2023-06-04 22:52:51,411] [INFO] Task started: Blastn
[2023-06-04 22:52:51,411] [INFO] Running command: blastn -query GCA_934167455.1_ERR7738551_bin.11_genomic.fna/markers.fasta -db /var/lib/cwl/stg39a0572b-c389-4633-a4bb-c9505223bbbf/dqc_reference/reference_markers_gtdb.fasta -out GCA_934167455.1_ERR7738551_bin.11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:52:52,184] [INFO] Task succeeded: Blastn
[2023-06-04 22:52:52,188] [INFO] Selected 17 target genomes.
[2023-06-04 22:52:52,188] [INFO] Target genome list was writen to GCA_934167455.1_ERR7738551_bin.11_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:52:52,196] [INFO] Task started: fastANI
[2023-06-04 22:52:52,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg59bf7822-06e6-470f-9052-47b6a44cd8fe/GCA_934167455.1_ERR7738551_bin.11_genomic.fna.gz --refList GCA_934167455.1_ERR7738551_bin.11_genomic.fna/target_genomes_gtdb.txt --output GCA_934167455.1_ERR7738551_bin.11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:52:56,480] [INFO] Task succeeded: fastANI
[2023-06-04 22:52:56,498] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:52:56,498] [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_900754285.1	s__CAG-269 sp900754285	97.8757	213	302	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.84	99.84	0.90	0.90	2	conclusive
GCA_001916035.1	s__CAG-269 sp001916035	84.5319	208	302	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.66	98.24	0.82	0.78	3	-
GCA_905203195.1	s__CAG-269 sp905203195	83.5723	111	302	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_900551615.1	s__CAG-269 sp900551615	79.6208	125	302	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.20	98.20	0.87	0.87	2	-
GCA_904384205.1	s__CAG-269 sp904384205	79.5854	126	302	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_904384245.1	s__CAG-269 sp904384245	79.5378	124	302	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	79.2092	118	302	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_014846485.1	s__CAG-269 sp014846485	79.1417	100	302	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_000438255.1	s__CAG-269 sp000438255	79.1364	118	302	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.47	98.35	0.85	0.83	3	-
GCA_000435535.1	s__CAG-269 sp000435535	78.9491	113	302	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.62	99.62	0.79	0.79	2	-
GCA_017410505.1	s__CAG-269 sp017410505	78.9223	113	302	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_904419095.1	s__CAG-269 sp904419095	78.7372	92	302	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	78.5302	106	302	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_017409455.1	s__CAG-269 sp017409455	78.2785	73	302	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_017434295.1	s__CAG-269 sp017434295	78.1798	71	302	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_900553125.1	s__CAG-269 sp900553125	78.0277	82	302	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_902760765.1	s__CAG-269 sp902760765	77.9336	74	302	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	-
--------------------------------------------------------------------------------
[2023-06-04 22:52:56,500] [INFO] GTDB search result was written to GCA_934167455.1_ERR7738551_bin.11_genomic.fna/result_gtdb.tsv
[2023-06-04 22:52:56,501] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:52:56,505] [INFO] DFAST_QC result json was written to GCA_934167455.1_ERR7738551_bin.11_genomic.fna/dqc_result.json
[2023-06-04 22:52:56,505] [INFO] DFAST_QC completed!
[2023-06-04 22:52:56,505] [INFO] Total running time: 0h0m34s