[2023-06-28 13:51:25,055] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:51:25,058] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:51:25,058] [INFO] DQC Reference Directory: /var/lib/cwl/stgf00bd197-691f-4812-93fa-27904e6a48d4/dqc_reference
[2023-06-28 13:51:26,248] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:51:26,248] [INFO] Task started: Prodigal
[2023-06-28 13:51:26,249] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4fa1a47-18e9-4fce-97a2-80e2ed21049a/GCA_944320315.1_E07_bin76_genomic.fna.gz | prodigal -d GCA_944320315.1_E07_bin76_genomic.fna/cds.fna -a GCA_944320315.1_E07_bin76_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:51:50,137] [INFO] Task succeeded: Prodigal
[2023-06-28 13:51:50,137] [INFO] Task started: HMMsearch
[2023-06-28 13:51:50,137] [INFO] Running command: hmmsearch --tblout GCA_944320315.1_E07_bin76_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf00bd197-691f-4812-93fa-27904e6a48d4/dqc_reference/reference_markers.hmm GCA_944320315.1_E07_bin76_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:51:50,373] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:51:50,375] [INFO] Found 6/6 markers.
[2023-06-28 13:51:50,414] [INFO] Query marker FASTA was written to GCA_944320315.1_E07_bin76_genomic.fna/markers.fasta
[2023-06-28 13:51:50,414] [INFO] Task started: Blastn
[2023-06-28 13:51:50,414] [INFO] Running command: blastn -query GCA_944320315.1_E07_bin76_genomic.fna/markers.fasta -db /var/lib/cwl/stgf00bd197-691f-4812-93fa-27904e6a48d4/dqc_reference/reference_markers.fasta -out GCA_944320315.1_E07_bin76_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:51:51,027] [INFO] Task succeeded: Blastn
[2023-06-28 13:51:51,031] [INFO] Selected 22 target genomes.
[2023-06-28 13:51:51,031] [INFO] Target genome list was writen to GCA_944320315.1_E07_bin76_genomic.fna/target_genomes.txt
[2023-06-28 13:51:51,032] [INFO] Task started: fastANI
[2023-06-28 13:51:51,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4fa1a47-18e9-4fce-97a2-80e2ed21049a/GCA_944320315.1_E07_bin76_genomic.fna.gz --refList GCA_944320315.1_E07_bin76_genomic.fna/target_genomes.txt --output GCA_944320315.1_E07_bin76_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:52:09,183] [INFO] Task succeeded: fastANI
[2023-06-28 13:52:09,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf00bd197-691f-4812-93fa-27904e6a48d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:52:09,184] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf00bd197-691f-4812-93fa-27904e6a48d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:52:09,201] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 13:52:09,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 13:52:09,202] [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 salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	99.2089	1492	1689	95	conclusive
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	80.6233	874	1689	95	below_threshold
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	78.851	371	1689	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	78.8339	380	1689	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_900106755.1	674529	674529	type	True	78.8187	419	1689	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_000226135.2	674529	674529	type	True	78.8091	419	1689	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	78.8089	376	1689	95	below_threshold
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	78.7198	400	1689	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	78.6859	403	1689	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	78.6324	403	1689	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_000169015.1	47678	47678	suspected-type	True	78.5916	352	1689	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	78.5496	351	1689	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	78.526	354	1689	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002222615.2	47678	47678	suspected-type	True	78.5221	353	1689	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	78.5186	348	1689	95	below_threshold
Bacteroides congonensis	strain=Marseille-P3132	GCA_900130125.1	1871006	1871006	type	True	78.4864	370	1689	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	78.4803	352	1689	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	78.3695	389	1689	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	78.3593	388	1689	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	78.316	392	1689	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	78.311	387	1689	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	78.3071	386	1689	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:52:09,204] [INFO] DFAST Taxonomy check result was written to GCA_944320315.1_E07_bin76_genomic.fna/tc_result.tsv
[2023-06-28 13:52:09,205] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:52:09,205] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:52:09,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf00bd197-691f-4812-93fa-27904e6a48d4/dqc_reference/checkm_data
[2023-06-28 13:52:09,206] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:52:09,253] [INFO] Task started: CheckM
[2023-06-28 13:52:09,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320315.1_E07_bin76_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320315.1_E07_bin76_genomic.fna/checkm_input GCA_944320315.1_E07_bin76_genomic.fna/checkm_result
[2023-06-28 13:53:17,082] [INFO] Task succeeded: CheckM
[2023-06-28 13:53:17,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.16%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:53:17,104] [INFO] ===== Completeness check finished =====
[2023-06-28 13:53:17,105] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:53:17,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320315.1_E07_bin76_genomic.fna/markers.fasta)
[2023-06-28 13:53:17,105] [INFO] Task started: Blastn
[2023-06-28 13:53:17,105] [INFO] Running command: blastn -query GCA_944320315.1_E07_bin76_genomic.fna/markers.fasta -db /var/lib/cwl/stgf00bd197-691f-4812-93fa-27904e6a48d4/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320315.1_E07_bin76_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:53:17,948] [INFO] Task succeeded: Blastn
[2023-06-28 13:53:17,952] [INFO] Selected 18 target genomes.
[2023-06-28 13:53:17,952] [INFO] Target genome list was writen to GCA_944320315.1_E07_bin76_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:53:17,953] [INFO] Task started: fastANI
[2023-06-28 13:53:17,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4fa1a47-18e9-4fce-97a2-80e2ed21049a/GCA_944320315.1_E07_bin76_genomic.fna.gz --refList GCA_944320315.1_E07_bin76_genomic.fna/target_genomes_gtdb.txt --output GCA_944320315.1_E07_bin76_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:53:36,754] [INFO] Task succeeded: fastANI
[2023-06-28 13:53:36,769] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:53:36,769] [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_000381365.1	s__Bacteroides salyersiae	99.2089	1492	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	conclusive
GCA_905193145.1	s__Odoribacter sp905193145	94.719	113	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000613465.1	s__Bacteroides nordii	80.6526	849	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.55	98.11	0.85	0.80	13	-
GCA_900762525.1	s__Bacteroides sp900762525	80.2752	694	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014385165.1	s__Bacteroides sp014385165	79.3526	471	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000025985.1	s__Bacteroides fragilis	78.8682	373	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	-
GCF_900106755.1	s__Bacteroides faecis	78.8187	419	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	78.7081	402	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_000210075.1	s__Bacteroides xylanisolvens	78.7077	385	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_002849695.1	s__Bacteroides fragilis_A	78.6251	364	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	-
GCF_000156195.1	s__Bacteroides finegoldii	78.5394	356	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCF_002222615.2	s__Bacteroides caccae	78.5107	354	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCF_903181435.1	s__Bacteroides sp900765785	78.4601	372	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	78.3891	401	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_012113595.1	s__Bacteroides sp012113595	78.3501	379	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314995.1	s__Bacteroides ovatus	78.3501	389	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_000517545.1	s__Bacteroides reticulotermitis	77.6586	243	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_900544675.1	s__Phocaeicola sp900544675	76.6552	90	1689	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.98	99.96	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-28 13:53:36,772] [INFO] GTDB search result was written to GCA_944320315.1_E07_bin76_genomic.fna/result_gtdb.tsv
[2023-06-28 13:53:36,772] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:53:36,777] [INFO] DFAST_QC result json was written to GCA_944320315.1_E07_bin76_genomic.fna/dqc_result.json
[2023-06-28 13:53:36,777] [INFO] DFAST_QC completed!
[2023-06-28 13:53:36,777] [INFO] Total running time: 0h2m12s