[2023-06-30 10:00:07,705] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:00:07,708] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:00:07,709] [INFO] DQC Reference Directory: /var/lib/cwl/stge3cc896b-dfe8-4a46-853e-1e3dae26f8d4/dqc_reference
[2023-06-30 10:00:09,009] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:00:09,011] [INFO] Task started: Prodigal
[2023-06-30 10:00:09,011] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d12134e-9386-4e41-81a2-08a8bd810516/GCA_900764355.1_SRS1596872_6_genomic.fna.gz | prodigal -d GCA_900764355.1_SRS1596872_6_genomic.fna/cds.fna -a GCA_900764355.1_SRS1596872_6_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:00:12,262] [INFO] Task succeeded: Prodigal
[2023-06-30 10:00:12,262] [INFO] Task started: HMMsearch
[2023-06-30 10:00:12,262] [INFO] Running command: hmmsearch --tblout GCA_900764355.1_SRS1596872_6_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3cc896b-dfe8-4a46-853e-1e3dae26f8d4/dqc_reference/reference_markers.hmm GCA_900764355.1_SRS1596872_6_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:00:12,468] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:00:12,470] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7d12134e-9386-4e41-81a2-08a8bd810516/GCA_900764355.1_SRS1596872_6_genomic.fna.gz]
[2023-06-30 10:00:12,491] [INFO] Query marker FASTA was written to GCA_900764355.1_SRS1596872_6_genomic.fna/markers.fasta
[2023-06-30 10:00:12,491] [INFO] Task started: Blastn
[2023-06-30 10:00:12,492] [INFO] Running command: blastn -query GCA_900764355.1_SRS1596872_6_genomic.fna/markers.fasta -db /var/lib/cwl/stge3cc896b-dfe8-4a46-853e-1e3dae26f8d4/dqc_reference/reference_markers.fasta -out GCA_900764355.1_SRS1596872_6_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:00:13,752] [INFO] Task succeeded: Blastn
[2023-06-30 10:00:13,757] [INFO] Selected 13 target genomes.
[2023-06-30 10:00:13,757] [INFO] Target genome list was writen to GCA_900764355.1_SRS1596872_6_genomic.fna/target_genomes.txt
[2023-06-30 10:00:13,790] [INFO] Task started: fastANI
[2023-06-30 10:00:13,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d12134e-9386-4e41-81a2-08a8bd810516/GCA_900764355.1_SRS1596872_6_genomic.fna.gz --refList GCA_900764355.1_SRS1596872_6_genomic.fna/target_genomes.txt --output GCA_900764355.1_SRS1596872_6_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:00:19,703] [INFO] Task succeeded: fastANI
[2023-06-30 10:00:19,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3cc896b-dfe8-4a46-853e-1e3dae26f8d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:00:19,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3cc896b-dfe8-4a46-853e-1e3dae26f8d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:00:19,713] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:00:19,713] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 10:00:19,713] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	81.1571	62	197	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.565	69	197	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.4185	54	197	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:00:19,715] [INFO] DFAST Taxonomy check result was written to GCA_900764355.1_SRS1596872_6_genomic.fna/tc_result.tsv
[2023-06-30 10:00:19,716] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:00:19,716] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:00:19,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3cc896b-dfe8-4a46-853e-1e3dae26f8d4/dqc_reference/checkm_data
[2023-06-30 10:00:19,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:00:19,754] [INFO] Task started: CheckM
[2023-06-30 10:00:19,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900764355.1_SRS1596872_6_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900764355.1_SRS1596872_6_genomic.fna/checkm_input GCA_900764355.1_SRS1596872_6_genomic.fna/checkm_result
[2023-06-30 10:00:37,421] [INFO] Task succeeded: CheckM
[2023-06-30 10:00:37,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.62%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 10:00:37,447] [INFO] ===== Completeness check finished =====
[2023-06-30 10:00:37,447] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:00:37,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900764355.1_SRS1596872_6_genomic.fna/markers.fasta)
[2023-06-30 10:00:37,448] [INFO] Task started: Blastn
[2023-06-30 10:00:37,448] [INFO] Running command: blastn -query GCA_900764355.1_SRS1596872_6_genomic.fna/markers.fasta -db /var/lib/cwl/stge3cc896b-dfe8-4a46-853e-1e3dae26f8d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_900764355.1_SRS1596872_6_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:00:38,360] [INFO] Task succeeded: Blastn
[2023-06-30 10:00:38,366] [INFO] Selected 12 target genomes.
[2023-06-30 10:00:38,366] [INFO] Target genome list was writen to GCA_900764355.1_SRS1596872_6_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:00:38,375] [INFO] Task started: fastANI
[2023-06-30 10:00:38,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d12134e-9386-4e41-81a2-08a8bd810516/GCA_900764355.1_SRS1596872_6_genomic.fna.gz --refList GCA_900764355.1_SRS1596872_6_genomic.fna/target_genomes_gtdb.txt --output GCA_900764355.1_SRS1596872_6_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:00:42,596] [INFO] Task succeeded: fastANI
[2023-06-30 10:00:42,610] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 10:00:42,611] [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
GCF_014297285.1	s__Dysosmobacter sp001916835	94.5339	113	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	96.98	96.30	0.86	0.70	9	-
GCA_900544105.1	s__Dysosmobacter sp900544105	91.6294	99	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.36	97.36	0.83	0.83	2	-
GCA_000435975.1	s__CAG-83 sp000435975	87.546	77	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.04	97.67	0.83	0.76	8	-
GCA_900542115.1	s__Dysosmobacter sp900542115	83.7001	77	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.37	98.19	0.79	0.78	3	-
GCA_018228685.1	s__CAG-83 sp001916855	83.6114	76	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	96.79	95.43	0.86	0.74	11	-
GCA_900550685.1	s__Dysosmobacter sp900550685	83.5694	77	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.83	98.83	0.76	0.76	2	-
GCA_900544615.1	s__Dysosmobacter sp900544615	83.5361	83	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017937405.1	s__Dysosmobacter sp017937405	79.5162	66	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547745.1	s__CAG-83 sp900547745	79.3734	55	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	99.22	99.21	0.93	0.91	3	-
GCA_902388735.1	s__CAG-83 sp902388735	79.1276	53	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-83	95.0	98.86	98.86	0.87	0.87	2	-
GCA_910584075.1	s__Dysosmobacter sp910584075	78.4579	63	197	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:00:42,614] [INFO] GTDB search result was written to GCA_900764355.1_SRS1596872_6_genomic.fna/result_gtdb.tsv
[2023-06-30 10:00:42,615] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:00:42,631] [INFO] DFAST_QC result json was written to GCA_900764355.1_SRS1596872_6_genomic.fna/dqc_result.json
[2023-06-30 10:00:42,632] [INFO] DFAST_QC completed!
[2023-06-30 10:00:42,632] [INFO] Total running time: 0h0m35s