[2023-06-05 23:02:50,806] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:02:50,807] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:02:50,808] [INFO] DQC Reference Directory: /var/lib/cwl/stg232ba333-9a84-4d8b-ad1a-375f16346a76/dqc_reference
[2023-06-05 23:02:51,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:02:51,929] [INFO] Task started: Prodigal
[2023-06-05 23:02:51,930] [INFO] Running command: gunzip -c /var/lib/cwl/stge3493cc0-17a4-4bee-8ba0-7b64e5308406/GCA_934167535.1_ERR7738515_bin.65_genomic.fna.gz | prodigal -d GCA_934167535.1_ERR7738515_bin.65_genomic.fna/cds.fna -a GCA_934167535.1_ERR7738515_bin.65_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:03:04,763] [INFO] Task succeeded: Prodigal
[2023-06-05 23:03:04,763] [INFO] Task started: HMMsearch
[2023-06-05 23:03:04,763] [INFO] Running command: hmmsearch --tblout GCA_934167535.1_ERR7738515_bin.65_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg232ba333-9a84-4d8b-ad1a-375f16346a76/dqc_reference/reference_markers.hmm GCA_934167535.1_ERR7738515_bin.65_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:03:04,945] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:03:04,946] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge3493cc0-17a4-4bee-8ba0-7b64e5308406/GCA_934167535.1_ERR7738515_bin.65_genomic.fna.gz]
[2023-06-05 23:03:04,986] [INFO] Query marker FASTA was written to GCA_934167535.1_ERR7738515_bin.65_genomic.fna/markers.fasta
[2023-06-05 23:03:04,987] [INFO] Task started: Blastn
[2023-06-05 23:03:04,987] [INFO] Running command: blastn -query GCA_934167535.1_ERR7738515_bin.65_genomic.fna/markers.fasta -db /var/lib/cwl/stg232ba333-9a84-4d8b-ad1a-375f16346a76/dqc_reference/reference_markers.fasta -out GCA_934167535.1_ERR7738515_bin.65_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:03:05,445] [INFO] Task succeeded: Blastn
[2023-06-05 23:03:05,450] [INFO] Selected 16 target genomes.
[2023-06-05 23:03:05,450] [INFO] Target genome list was writen to GCA_934167535.1_ERR7738515_bin.65_genomic.fna/target_genomes.txt
[2023-06-05 23:03:05,451] [INFO] Task started: fastANI
[2023-06-05 23:03:05,452] [INFO] Running command: fastANI --query /var/lib/cwl/stge3493cc0-17a4-4bee-8ba0-7b64e5308406/GCA_934167535.1_ERR7738515_bin.65_genomic.fna.gz --refList GCA_934167535.1_ERR7738515_bin.65_genomic.fna/target_genomes.txt --output GCA_934167535.1_ERR7738515_bin.65_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:03:16,173] [INFO] Task succeeded: fastANI
[2023-06-05 23:03:16,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg232ba333-9a84-4d8b-ad1a-375f16346a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:03:16,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg232ba333-9a84-4d8b-ad1a-375f16346a76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:03:16,183] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 23:03:16,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 23:03:16,184] [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 cutis	strain=Marseille-P4118	GCA_900241005.1	2024197	2024197	type	True	98.9734	518	767	95	conclusive
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	79.3234	228	767	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.3101	231	767	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	79.3004	233	767	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	79.0791	184	767	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.0043	190	767	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	78.9433	242	767	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	78.8462	180	767	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	78.7424	183	767	95	below_threshold
Bacteroides fluxus	strain=YIT 12057	GCA_000195635.1	626930	626930	type	True	78.5314	221	767	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	78.471	193	767	95	below_threshold
Bacteroides helcogenes	strain=P 36-108	GCA_000186225.1	290053	290053	type	True	78.1638	183	767	95	below_threshold
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	77.747	185	767	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	77.6305	206	767	95	below_threshold
Bacteroides salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	76.8394	108	767	95	below_threshold
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	76.5044	104	767	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 23:03:16,185] [INFO] DFAST Taxonomy check result was written to GCA_934167535.1_ERR7738515_bin.65_genomic.fna/tc_result.tsv
[2023-06-05 23:03:16,186] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:03:16,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:03:16,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg232ba333-9a84-4d8b-ad1a-375f16346a76/dqc_reference/checkm_data
[2023-06-05 23:03:16,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:03:16,226] [INFO] Task started: CheckM
[2023-06-05 23:03:16,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934167535.1_ERR7738515_bin.65_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934167535.1_ERR7738515_bin.65_genomic.fna/checkm_input GCA_934167535.1_ERR7738515_bin.65_genomic.fna/checkm_result
[2023-06-05 23:03:54,846] [INFO] Task succeeded: CheckM
[2023-06-05 23:03:54,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 23:03:54,863] [INFO] ===== Completeness check finished =====
[2023-06-05 23:03:54,863] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:03:54,864] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934167535.1_ERR7738515_bin.65_genomic.fna/markers.fasta)
[2023-06-05 23:03:54,865] [INFO] Task started: Blastn
[2023-06-05 23:03:54,865] [INFO] Running command: blastn -query GCA_934167535.1_ERR7738515_bin.65_genomic.fna/markers.fasta -db /var/lib/cwl/stg232ba333-9a84-4d8b-ad1a-375f16346a76/dqc_reference/reference_markers_gtdb.fasta -out GCA_934167535.1_ERR7738515_bin.65_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:03:55,283] [INFO] Task succeeded: Blastn
[2023-06-05 23:03:55,286] [INFO] Selected 14 target genomes.
[2023-06-05 23:03:55,286] [INFO] Target genome list was writen to GCA_934167535.1_ERR7738515_bin.65_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:03:55,288] [INFO] Task started: fastANI
[2023-06-05 23:03:55,289] [INFO] Running command: fastANI --query /var/lib/cwl/stge3493cc0-17a4-4bee-8ba0-7b64e5308406/GCA_934167535.1_ERR7738515_bin.65_genomic.fna.gz --refList GCA_934167535.1_ERR7738515_bin.65_genomic.fna/target_genomes_gtdb.txt --output GCA_934167535.1_ERR7738515_bin.65_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:04:06,042] [INFO] Task succeeded: fastANI
[2023-06-05 23:04:06,051] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 23:04:06,051] [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_900241005.1	s__Bacteroides cutis	98.9734	518	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.53	99.47	0.92	0.89	5	conclusive
GCA_905215345.1	s__Bacteroides sp905215345	79.3532	251	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154525.1	s__Bacteroides stercoris	79.2893	234	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_900129655.1	s__Bacteroides clarus	79.0441	246	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCF_003438615.1	s__Bacteroides sp003545565	78.8859	239	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000374365.1	s__Bacteroides gallinarum	78.8462	180	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000195635.1	s__Bacteroides fluxus	78.5232	222	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_000186225.1	s__Bacteroides helcogenes	78.1638	183	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902364365.1	s__Bacteroides sp900556215	77.8976	195	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCF_000513195.1	s__Bacteroides timonensis	77.7297	186	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000158035.1	s__Bacteroides cellulosilyticus	77.6305	206	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.21	95.02	0.83	0.72	42	-
GCF_009193325.2	s__Bacteroides zhangwenhongi	77.2567	107	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	97.65	96.82	0.72	0.66	9	-
GCF_000381365.1	s__Bacteroides salyersiae	76.8394	108	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCA_900556625.1	s__Bacteroides sp900556625	76.3526	62	767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.84	99.84	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-05 23:04:06,053] [INFO] GTDB search result was written to GCA_934167535.1_ERR7738515_bin.65_genomic.fna/result_gtdb.tsv
[2023-06-05 23:04:06,054] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:04:06,057] [INFO] DFAST_QC result json was written to GCA_934167535.1_ERR7738515_bin.65_genomic.fna/dqc_result.json
[2023-06-05 23:04:06,057] [INFO] DFAST_QC completed!
[2023-06-05 23:04:06,057] [INFO] Total running time: 0h1m15s