[2023-06-05 02:54:31,957] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:54:31,959] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:54:31,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg02d68495-4338-441e-9a4f-4207001e3ac0/dqc_reference
[2023-06-05 02:54:33,303] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:54:33,308] [INFO] Task started: Prodigal
[2023-06-05 02:54:33,308] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d01ea85-d7cf-43ec-ab1c-c1fcfb0e79b0/GCA_004562535.1_ASM456253v1_genomic.fna.gz | prodigal -d GCA_004562535.1_ASM456253v1_genomic.fna/cds.fna -a GCA_004562535.1_ASM456253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:54:37,656] [INFO] Task succeeded: Prodigal
[2023-06-05 02:54:37,656] [INFO] Task started: HMMsearch
[2023-06-05 02:54:37,656] [INFO] Running command: hmmsearch --tblout GCA_004562535.1_ASM456253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02d68495-4338-441e-9a4f-4207001e3ac0/dqc_reference/reference_markers.hmm GCA_004562535.1_ASM456253v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:54:37,904] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:54:37,905] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9d01ea85-d7cf-43ec-ab1c-c1fcfb0e79b0/GCA_004562535.1_ASM456253v1_genomic.fna.gz]
[2023-06-05 02:54:37,937] [INFO] Query marker FASTA was written to GCA_004562535.1_ASM456253v1_genomic.fna/markers.fasta
[2023-06-05 02:54:37,938] [INFO] Task started: Blastn
[2023-06-05 02:54:37,938] [INFO] Running command: blastn -query GCA_004562535.1_ASM456253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d68495-4338-441e-9a4f-4207001e3ac0/dqc_reference/reference_markers.fasta -out GCA_004562535.1_ASM456253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:54:38,518] [INFO] Task succeeded: Blastn
[2023-06-05 02:54:38,522] [INFO] Selected 19 target genomes.
[2023-06-05 02:54:38,522] [INFO] Target genome list was writen to GCA_004562535.1_ASM456253v1_genomic.fna/target_genomes.txt
[2023-06-05 02:54:38,524] [INFO] Task started: fastANI
[2023-06-05 02:54:38,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d01ea85-d7cf-43ec-ab1c-c1fcfb0e79b0/GCA_004562535.1_ASM456253v1_genomic.fna.gz --refList GCA_004562535.1_ASM456253v1_genomic.fna/target_genomes.txt --output GCA_004562535.1_ASM456253v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:54:52,874] [INFO] Task succeeded: fastANI
[2023-06-05 02:54:52,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02d68495-4338-441e-9a4f-4207001e3ac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:54:52,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02d68495-4338-441e-9a4f-4207001e3ac0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:54:52,882] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:54:52,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:54:52,883] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	79.3868	65	478	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.5225	68	478	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.3001	80	478	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.9429	83	478	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:54:52,886] [INFO] DFAST Taxonomy check result was written to GCA_004562535.1_ASM456253v1_genomic.fna/tc_result.tsv
[2023-06-05 02:54:52,886] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:54:52,887] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:54:52,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02d68495-4338-441e-9a4f-4207001e3ac0/dqc_reference/checkm_data
[2023-06-05 02:54:52,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:54:52,913] [INFO] Task started: CheckM
[2023-06-05 02:54:52,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004562535.1_ASM456253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004562535.1_ASM456253v1_genomic.fna/checkm_input GCA_004562535.1_ASM456253v1_genomic.fna/checkm_result
[2023-06-05 02:55:13,255] [INFO] Task succeeded: CheckM
[2023-06-05 02:55:13,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.35%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:55:13,276] [INFO] ===== Completeness check finished =====
[2023-06-05 02:55:13,277] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:55:13,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004562535.1_ASM456253v1_genomic.fna/markers.fasta)
[2023-06-05 02:55:13,278] [INFO] Task started: Blastn
[2023-06-05 02:55:13,278] [INFO] Running command: blastn -query GCA_004562535.1_ASM456253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d68495-4338-441e-9a4f-4207001e3ac0/dqc_reference/reference_markers_gtdb.fasta -out GCA_004562535.1_ASM456253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:55:14,143] [INFO] Task succeeded: Blastn
[2023-06-05 02:55:14,148] [INFO] Selected 25 target genomes.
[2023-06-05 02:55:14,149] [INFO] Target genome list was writen to GCA_004562535.1_ASM456253v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:55:14,157] [INFO] Task started: fastANI
[2023-06-05 02:55:14,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d01ea85-d7cf-43ec-ab1c-c1fcfb0e79b0/GCA_004562535.1_ASM456253v1_genomic.fna.gz --refList GCA_004562535.1_ASM456253v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004562535.1_ASM456253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:55:23,185] [INFO] Task succeeded: fastANI
[2023-06-05 02:55:23,212] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 02:55:23,212] [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_902778275.1	s__Limivicinus sp902778275	79.8401	182	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470325.1	s__Limivicinus sp017470325	79.6666	172	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316205.1	s__Limivicinus sp900316205	79.549	164	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.11	98.31	0.88	0.81	3	-
GCA_017428565.1	s__Limivicinus sp017428565	79.5359	173	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775985.1	s__Limivicinus sp902775985	79.4904	171	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.70	98.45	0.76	0.73	5	-
GCA_017545165.1	s__Limivicinus sp017545165	79.4745	144	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765595.1	s__Limivicinus sp002350825	79.4438	180	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.80	99.80	0.90	0.90	2	-
GCA_900316255.1	s__Limivicinus sp900316255	79.4413	166	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.92	95.41	0.88	0.79	4	-
GCA_902786615.1	s__Limivicinus sp902786615	79.2643	130	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319835.1	s__Limivicinus sp900319835	79.1368	156	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902778285.1	s__Limivicinus sp902778285	79.029	167	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.33	98.33	0.79	0.79	2	-
GCA_902791215.1	s__Limivicinus sp902791215	79.0251	134	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793285.1	s__Limivicinus sp902793285	78.8381	125	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.34	97.34	0.78	0.78	2	-
GCA_017477695.1	s__Limivicinus sp017477695	78.8105	134	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785905.1	s__Limivicinus sp902785905	78.8	127	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761635.1	s__Limivicinus sp902761635	78.683	128	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549645.1	s__Limivicinus sp900549645	78.5138	136	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.52	99.05	0.92	0.86	3	-
GCA_902789745.1	s__Limivicinus sp902789745	78.4155	123	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547315.1	s__Limivicinus sp900547315	78.3599	142	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.47	98.42	0.88	0.83	3	-
GCA_003150355.1	s__Limivicinus sp003150355	78.3509	114	478	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.34	96.94	0.74	0.68	6	-
--------------------------------------------------------------------------------
[2023-06-05 02:55:23,214] [INFO] GTDB search result was written to GCA_004562535.1_ASM456253v1_genomic.fna/result_gtdb.tsv
[2023-06-05 02:55:23,215] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:55:23,219] [INFO] DFAST_QC result json was written to GCA_004562535.1_ASM456253v1_genomic.fna/dqc_result.json
[2023-06-05 02:55:23,219] [INFO] DFAST_QC completed!
[2023-06-05 02:55:23,219] [INFO] Total running time: 0h0m51s