[2023-06-08 09:17:07,774] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:17:07,779] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:17:07,779] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7fbcc5a-9d71-4859-a289-6d02e577d0ea/dqc_reference
[2023-06-08 09:17:10,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:17:10,151] [INFO] Task started: Prodigal
[2023-06-08 09:17:10,151] [INFO] Running command: gunzip -c /var/lib/cwl/stge038bbc1-19cb-4684-9096-91b96f19580d/GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:17:23,447] [INFO] Task succeeded: Prodigal
[2023-06-08 09:17:23,448] [INFO] Task started: HMMsearch
[2023-06-08 09:17:23,448] [INFO] Running command: hmmsearch --tblout GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7fbcc5a-9d71-4859-a289-6d02e577d0ea/dqc_reference/reference_markers.hmm GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:17:23,683] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:17:23,685] [INFO] Found 6/6 markers.
[2023-06-08 09:17:23,716] [INFO] Query marker FASTA was written to GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:17:23,716] [INFO] Task started: Blastn
[2023-06-08 09:17:23,717] [INFO] Running command: blastn -query GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7fbcc5a-9d71-4859-a289-6d02e577d0ea/dqc_reference/reference_markers.fasta -out GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:17:25,034] [INFO] Task succeeded: Blastn
[2023-06-08 09:17:25,040] [INFO] Selected 29 target genomes.
[2023-06-08 09:17:25,041] [INFO] Target genome list was writen to GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:17:25,050] [INFO] Task started: fastANI
[2023-06-08 09:17:25,050] [INFO] Running command: fastANI --query /var/lib/cwl/stge038bbc1-19cb-4684-9096-91b96f19580d/GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:17:41,627] [INFO] Task succeeded: fastANI
[2023-06-08 09:17:41,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7fbcc5a-9d71-4859-a289-6d02e577d0ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:17:41,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7fbcc5a-9d71-4859-a289-6d02e577d0ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:17:41,630] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:17:41,630] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:17:41,631] [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
--------------------------------------------------------------------------------
[2023-06-08 09:17:41,633] [INFO] DFAST Taxonomy check result was written to GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:17:41,634] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:17:41,634] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:17:41,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7fbcc5a-9d71-4859-a289-6d02e577d0ea/dqc_reference/checkm_data
[2023-06-08 09:17:41,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:17:41,672] [INFO] Task started: CheckM
[2023-06-08 09:17:41,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:18:22,852] [INFO] Task succeeded: CheckM
[2023-06-08 09:18:22,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:18:22,872] [INFO] ===== Completeness check finished =====
[2023-06-08 09:18:22,872] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:18:22,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:18:22,873] [INFO] Task started: Blastn
[2023-06-08 09:18:22,873] [INFO] Running command: blastn -query GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7fbcc5a-9d71-4859-a289-6d02e577d0ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:18:23,678] [INFO] Task succeeded: Blastn
[2023-06-08 09:18:23,683] [INFO] Selected 17 target genomes.
[2023-06-08 09:18:23,683] [INFO] Target genome list was writen to GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:18:23,691] [INFO] Task started: fastANI
[2023-06-08 09:18:23,691] [INFO] Running command: fastANI --query /var/lib/cwl/stge038bbc1-19cb-4684-9096-91b96f19580d/GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:18:30,587] [INFO] Task succeeded: fastANI
[2023-06-08 09:18:30,603] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:18:30,604] [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_004552615.1	s__Cryptobacteroides sp004552615	98.8807	508	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.38	98.38	0.80	0.80	2	conclusive
GCA_900769145.1	s__Cryptobacteroides sp900769145	79.6815	275	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004552115.1	s__Cryptobacteroides sp004552115	79.2175	200	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.49	98.12	0.74	0.72	3	-
GCA_000434935.1	s__Cryptobacteroides sp000434935	78.3906	173	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.20	96.88	0.85	0.83	4	-
GCA_900546925.1	s__Cryptobacteroides sp900546925	78.0432	120	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.81	98.70	0.85	0.79	6	-
GCA_000435075.1	s__Cryptobacteroides sp000435075	78.0002	163	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.30	97.06	0.87	0.85	4	-
GCA_000432515.1	s__Cryptobacteroides sp000432515	77.9509	184	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.23	97.18	0.82	0.82	4	-
GCA_017627955.1	s__Cryptobacteroides sp017627955	77.2379	51	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319855.1	s__Cryptobacteroides sp900319855	76.9121	63	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.60	97.81	0.89	0.84	6	-
GCA_018066065.1	s__Cryptobacteroides sp018066065	76.6609	70	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399905.1	s__Cryptobacteroides sp017399905	76.3116	55	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.58	97.58	0.79	0.79	2	-
GCA_902803715.1	s__Cryptobacteroides sp902803715	76.0557	66	741	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.42	97.90	0.88	0.86	3	-
--------------------------------------------------------------------------------
[2023-06-08 09:18:30,606] [INFO] GTDB search result was written to GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:18:30,606] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:18:30,609] [INFO] DFAST_QC result json was written to GCA_945948495.1_SRR15057922_bin.29_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:18:30,609] [INFO] DFAST_QC completed!
[2023-06-08 09:18:30,609] [INFO] Total running time: 0h1m23s