[2023-06-05 11:05:55,109] [INFO] DFAST_QC pipeline started.
[2023-06-05 11:05:55,112] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 11:05:55,112] [INFO] DQC Reference Directory: /var/lib/cwl/stgaed284b5-2577-4f54-a37c-2fb3603362e9/dqc_reference
[2023-06-05 11:05:57,361] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 11:05:57,362] [INFO] Task started: Prodigal
[2023-06-05 11:05:57,363] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1d6c8cb-6109-448d-a69a-896a4ccfd04b/GCA_934839505.1_MTG231_bin.20.fa_genomic.fna.gz | prodigal -d GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/cds.fna -a GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 11:06:11,846] [INFO] Task succeeded: Prodigal
[2023-06-05 11:06:11,847] [INFO] Task started: HMMsearch
[2023-06-05 11:06:11,847] [INFO] Running command: hmmsearch --tblout GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaed284b5-2577-4f54-a37c-2fb3603362e9/dqc_reference/reference_markers.hmm GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 11:06:12,080] [INFO] Task succeeded: HMMsearch
[2023-06-05 11:06:12,081] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb1d6c8cb-6109-448d-a69a-896a4ccfd04b/GCA_934839505.1_MTG231_bin.20.fa_genomic.fna.gz]
[2023-06-05 11:06:12,111] [INFO] Query marker FASTA was written to GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/markers.fasta
[2023-06-05 11:06:12,112] [INFO] Task started: Blastn
[2023-06-05 11:06:12,112] [INFO] Running command: blastn -query GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgaed284b5-2577-4f54-a37c-2fb3603362e9/dqc_reference/reference_markers.fasta -out GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 11:06:12,692] [INFO] Task succeeded: Blastn
[2023-06-05 11:06:12,697] [INFO] Selected 17 target genomes.
[2023-06-05 11:06:12,697] [INFO] Target genome list was writen to GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/target_genomes.txt
[2023-06-05 11:06:12,701] [INFO] Task started: fastANI
[2023-06-05 11:06:12,701] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1d6c8cb-6109-448d-a69a-896a4ccfd04b/GCA_934839505.1_MTG231_bin.20.fa_genomic.fna.gz --refList GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/target_genomes.txt --output GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 11:06:24,364] [INFO] Task succeeded: fastANI
[2023-06-05 11:06:24,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaed284b5-2577-4f54-a37c-2fb3603362e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 11:06:24,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaed284b5-2577-4f54-a37c-2fb3603362e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 11:06:24,381] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2023-06-05 11:06:24,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 11:06:24,381] [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
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	98.8747	797	910	95	conclusive
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	98.8121	807	910	95	conclusive
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	90.698	747	910	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	82.5734	143	910	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	82.447	143	910	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	82.3473	142	910	95	below_threshold
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	80.5876	417	910	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	80.5835	408	910	95	below_threshold
Phocaeicola sartorii	strain=JCM 17136	GCA_000614185.1	671267	671267	type	True	80.5099	410	910	95	below_threshold
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	80.4937	418	910	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	80.434	417	910	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	80.395	425	910	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	78.5638	130	910	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	78.5105	130	910	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	78.4777	128	910	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	78.4629	149	910	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 11:06:24,384] [INFO] DFAST Taxonomy check result was written to GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/tc_result.tsv
[2023-06-05 11:06:24,384] [INFO] ===== Taxonomy check completed =====
[2023-06-05 11:06:24,384] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 11:06:24,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaed284b5-2577-4f54-a37c-2fb3603362e9/dqc_reference/checkm_data
[2023-06-05 11:06:24,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 11:06:24,413] [INFO] Task started: CheckM
[2023-06-05 11:06:24,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/checkm_input GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/checkm_result
[2023-06-05 11:07:08,617] [INFO] Task succeeded: CheckM
[2023-06-05 11:07:08,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 11:07:08,639] [INFO] ===== Completeness check finished =====
[2023-06-05 11:07:08,640] [INFO] ===== Start GTDB Search =====
[2023-06-05 11:07:08,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/markers.fasta)
[2023-06-05 11:07:08,640] [INFO] Task started: Blastn
[2023-06-05 11:07:08,641] [INFO] Running command: blastn -query GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgaed284b5-2577-4f54-a37c-2fb3603362e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 11:07:09,424] [INFO] Task succeeded: Blastn
[2023-06-05 11:07:09,429] [INFO] Selected 14 target genomes.
[2023-06-05 11:07:09,429] [INFO] Target genome list was writen to GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 11:07:09,435] [INFO] Task started: fastANI
[2023-06-05 11:07:09,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1d6c8cb-6109-448d-a69a-896a4ccfd04b/GCA_934839505.1_MTG231_bin.20.fa_genomic.fna.gz --refList GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 11:07:19,749] [INFO] Task succeeded: fastANI
[2023-06-05 11:07:19,764] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 11:07:19,764] [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_000382445.1	s__Phocaeicola massiliensis	98.8121	807	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.84	98.03	0.86	0.62	25	conclusive
GCA_900760795.1	s__Phocaeicola sp900760795	92.428	546	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493165.1	s__Phocaeicola sp002493165	90.6519	687	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.20	98.75	0.86	0.83	5	-
GCF_000154525.1	s__Bacteroides stercoris	82.3529	145	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_000012825.1	s__Phocaeicola vulgatus	80.5044	416	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	98.84	95.43	0.81	0.61	263	-
GCF_000614185.1	s__Phocaeicola sartorii	80.4943	411	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.95	98.44	0.85	0.76	7	-
GCF_013009555.1	s__Phocaeicola dorei	80.434	417	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	99.04	97.27	0.84	0.54	104	-
GCA_011959205.1	s__Phocaeicola sp011959205	80.0605	365	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.90	0.90	2	-
GCA_902388365.1	s__Phocaeicola sp902388365	80.0284	412	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.75	97.52	0.90	0.83	3	-
GCF_900129655.1	s__Bacteroides clarus	78.5638	130	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.75	98.47	0.87	0.82	18	-
GCA_910578895.1	s__Bacteroides sp910578895	78.3622	111	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374365.1	s__Bacteroides gallinarum	78.2143	107	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_003438615.1	s__Bacteroides sp003545565	78.0865	126	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_012113595.1	s__Bacteroides sp012113595	76.8343	157	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 11:07:19,766] [INFO] GTDB search result was written to GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 11:07:19,767] [INFO] ===== GTDB Search completed =====
[2023-06-05 11:07:19,775] [INFO] DFAST_QC result json was written to GCA_934839505.1_MTG231_bin.20.fa_genomic.fna/dqc_result.json
[2023-06-05 11:07:19,776] [INFO] DFAST_QC completed!
[2023-06-05 11:07:19,776] [INFO] Total running time: 0h1m25s