[2024-01-24 13:22:02,075] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:02,077] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:02,077] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc3ee5e8-1d66-4ed4-9cac-ea5aaf86db87/dqc_reference
[2024-01-24 13:22:03,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:03,444] [INFO] Task started: Prodigal
[2024-01-24 13:22:03,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg91f5f399-1144-4f18-8720-718eecdd4314/GCF_004793475.1_ASM479347v1_genomic.fna.gz | prodigal -d GCF_004793475.1_ASM479347v1_genomic.fna/cds.fna -a GCF_004793475.1_ASM479347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:29,261] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:29,261] [INFO] Task started: HMMsearch
[2024-01-24 13:22:29,261] [INFO] Running command: hmmsearch --tblout GCF_004793475.1_ASM479347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc3ee5e8-1d66-4ed4-9cac-ea5aaf86db87/dqc_reference/reference_markers.hmm GCF_004793475.1_ASM479347v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:29,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:29,559] [INFO] Found 6/6 markers.
[2024-01-24 13:22:29,599] [INFO] Query marker FASTA was written to GCF_004793475.1_ASM479347v1_genomic.fna/markers.fasta
[2024-01-24 13:22:29,600] [INFO] Task started: Blastn
[2024-01-24 13:22:29,600] [INFO] Running command: blastn -query GCF_004793475.1_ASM479347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc3ee5e8-1d66-4ed4-9cac-ea5aaf86db87/dqc_reference/reference_markers.fasta -out GCF_004793475.1_ASM479347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:30,225] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:30,228] [INFO] Selected 9 target genomes.
[2024-01-24 13:22:30,229] [INFO] Target genome list was writen to GCF_004793475.1_ASM479347v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:30,244] [INFO] Task started: fastANI
[2024-01-24 13:22:30,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg91f5f399-1144-4f18-8720-718eecdd4314/GCF_004793475.1_ASM479347v1_genomic.fna.gz --refList GCF_004793475.1_ASM479347v1_genomic.fna/target_genomes.txt --output GCF_004793475.1_ASM479347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:39,191] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:39,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc3ee5e8-1d66-4ed4-9cac-ea5aaf86db87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:39,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc3ee5e8-1d66-4ed4-9cac-ea5aaf86db87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:39,202] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:39,203] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:39,203] [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
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	98.0453	1089	1396	95	conclusive
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	92.1781	906	1396	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	92.134	907	1396	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	92.1119	926	1396	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	92.0597	915	1396	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	91.6956	896	1396	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	90.9144	879	1396	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.2296	540	1396	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.6512	491	1396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:39,204] [INFO] DFAST Taxonomy check result was written to GCF_004793475.1_ASM479347v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:39,205] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:39,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:39,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc3ee5e8-1d66-4ed4-9cac-ea5aaf86db87/dqc_reference/checkm_data
[2024-01-24 13:22:39,207] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:39,256] [INFO] Task started: CheckM
[2024-01-24 13:22:39,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004793475.1_ASM479347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004793475.1_ASM479347v1_genomic.fna/checkm_input GCF_004793475.1_ASM479347v1_genomic.fna/checkm_result
[2024-01-24 13:23:48,360] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:48,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:48,381] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:48,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:48,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004793475.1_ASM479347v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:48,382] [INFO] Task started: Blastn
[2024-01-24 13:23:48,383] [INFO] Running command: blastn -query GCF_004793475.1_ASM479347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc3ee5e8-1d66-4ed4-9cac-ea5aaf86db87/dqc_reference/reference_markers_gtdb.fasta -out GCF_004793475.1_ASM479347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:49,217] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:49,220] [INFO] Selected 11 target genomes.
[2024-01-24 13:23:49,220] [INFO] Target genome list was writen to GCF_004793475.1_ASM479347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:49,232] [INFO] Task started: fastANI
[2024-01-24 13:23:49,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg91f5f399-1144-4f18-8720-718eecdd4314/GCF_004793475.1_ASM479347v1_genomic.fna.gz --refList GCF_004793475.1_ASM479347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004793475.1_ASM479347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:58,688] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:58,703] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:58,704] [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_004793475.1	s__Bacteroides sp002491635	100.0	1391	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	conclusive
GCF_000154205.1	s__Bacteroides uniformis	92.0597	915	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	-
GCF_000614125.1	s__Bacteroides rodentium	90.9008	880	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905197435.1	s__Bacteroides sp905197435	86.4257	571	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195635.1	s__Bacteroides fluxus	81.5653	661	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCA_902388495.1	s__Bacteroides sp902388495	81.1132	616	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCA_905203765.1	s__Bacteroides sp905203765	80.3447	432	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129655.1	s__Bacteroides clarus	80.1265	500	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_000155815.1	s__Bacteroides eggerthii	79.8549	498	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCF_004342845.1	s__Bacteroides heparinolyticus	79.77	480	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCF_000186225.1	s__Bacteroides helcogenes	79.6012	522	1396	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:58,706] [INFO] GTDB search result was written to GCF_004793475.1_ASM479347v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:58,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:58,710] [INFO] DFAST_QC result json was written to GCF_004793475.1_ASM479347v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:58,710] [INFO] DFAST_QC completed!
[2024-01-24 13:23:58,710] [INFO] Total running time: 0h1m57s