[2023-06-05 08:20:14,395] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:20:14,398] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:20:14,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg97afe59f-470d-46a6-9297-8a6050793ebc/dqc_reference
[2023-06-05 08:20:16,651] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:20:16,652] [INFO] Task started: Prodigal
[2023-06-05 08:20:16,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg84ff22b5-ae09-4197-a5c8-b76643ebc1c4/GCA_934692435.1_ERR7747782_bin.13_genomic.fna.gz | prodigal -d GCA_934692435.1_ERR7747782_bin.13_genomic.fna/cds.fna -a GCA_934692435.1_ERR7747782_bin.13_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:20:32,553] [INFO] Task succeeded: Prodigal
[2023-06-05 08:20:32,554] [INFO] Task started: HMMsearch
[2023-06-05 08:20:32,554] [INFO] Running command: hmmsearch --tblout GCA_934692435.1_ERR7747782_bin.13_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97afe59f-470d-46a6-9297-8a6050793ebc/dqc_reference/reference_markers.hmm GCA_934692435.1_ERR7747782_bin.13_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:20:32,824] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:20:32,825] [INFO] Found 6/6 markers.
[2023-06-05 08:20:32,858] [INFO] Query marker FASTA was written to GCA_934692435.1_ERR7747782_bin.13_genomic.fna/markers.fasta
[2023-06-05 08:20:32,858] [INFO] Task started: Blastn
[2023-06-05 08:20:32,858] [INFO] Running command: blastn -query GCA_934692435.1_ERR7747782_bin.13_genomic.fna/markers.fasta -db /var/lib/cwl/stg97afe59f-470d-46a6-9297-8a6050793ebc/dqc_reference/reference_markers.fasta -out GCA_934692435.1_ERR7747782_bin.13_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:20:33,455] [INFO] Task succeeded: Blastn
[2023-06-05 08:20:33,461] [INFO] Selected 19 target genomes.
[2023-06-05 08:20:33,462] [INFO] Target genome list was writen to GCA_934692435.1_ERR7747782_bin.13_genomic.fna/target_genomes.txt
[2023-06-05 08:20:33,463] [INFO] Task started: fastANI
[2023-06-05 08:20:33,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg84ff22b5-ae09-4197-a5c8-b76643ebc1c4/GCA_934692435.1_ERR7747782_bin.13_genomic.fna.gz --refList GCA_934692435.1_ERR7747782_bin.13_genomic.fna/target_genomes.txt --output GCA_934692435.1_ERR7747782_bin.13_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:20:45,051] [INFO] Task succeeded: fastANI
[2023-06-05 08:20:45,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97afe59f-470d-46a6-9297-8a6050793ebc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:20:45,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97afe59f-470d-46a6-9297-8a6050793ebc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:20:45,075] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:20:45,075] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 08:20:45,075] [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 coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	79.4365	239	1090	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	79.3906	220	1090	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	79.0655	220	1090	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.8564	176	1090	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.7274	184	1090	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	78.6616	220	1090	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	78.5925	220	1090	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	77.7334	116	1090	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.7318	113	1090	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	77.6105	127	1090	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	77.575	126	1090	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	77.5242	102	1090	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	77.5153	189	1090	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	77.515	125	1090	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 08:20:45,077] [INFO] DFAST Taxonomy check result was written to GCA_934692435.1_ERR7747782_bin.13_genomic.fna/tc_result.tsv
[2023-06-05 08:20:45,078] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:20:45,078] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:20:45,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97afe59f-470d-46a6-9297-8a6050793ebc/dqc_reference/checkm_data
[2023-06-05 08:20:45,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:20:45,117] [INFO] Task started: CheckM
[2023-06-05 08:20:45,118] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934692435.1_ERR7747782_bin.13_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934692435.1_ERR7747782_bin.13_genomic.fna/checkm_input GCA_934692435.1_ERR7747782_bin.13_genomic.fna/checkm_result
[2023-06-05 08:21:31,835] [INFO] Task succeeded: CheckM
[2023-06-05 08:21:31,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:21:31,858] [INFO] ===== Completeness check finished =====
[2023-06-05 08:21:31,859] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:21:31,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934692435.1_ERR7747782_bin.13_genomic.fna/markers.fasta)
[2023-06-05 08:21:31,859] [INFO] Task started: Blastn
[2023-06-05 08:21:31,859] [INFO] Running command: blastn -query GCA_934692435.1_ERR7747782_bin.13_genomic.fna/markers.fasta -db /var/lib/cwl/stg97afe59f-470d-46a6-9297-8a6050793ebc/dqc_reference/reference_markers_gtdb.fasta -out GCA_934692435.1_ERR7747782_bin.13_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:21:32,703] [INFO] Task succeeded: Blastn
[2023-06-05 08:21:32,708] [INFO] Selected 17 target genomes.
[2023-06-05 08:21:32,708] [INFO] Target genome list was writen to GCA_934692435.1_ERR7747782_bin.13_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:21:32,717] [INFO] Task started: fastANI
[2023-06-05 08:21:32,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg84ff22b5-ae09-4197-a5c8-b76643ebc1c4/GCA_934692435.1_ERR7747782_bin.13_genomic.fna.gz --refList GCA_934692435.1_ERR7747782_bin.13_genomic.fna/target_genomes_gtdb.txt --output GCA_934692435.1_ERR7747782_bin.13_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:21:42,595] [INFO] Task succeeded: fastANI
[2023-06-05 08:21:42,613] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:21:42,613] [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_000434735.1	s__Phocaeicola sp000434735	95.6698	888	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.56	97.52	0.82	0.81	3	conclusive
GCF_000154845.1	s__Phocaeicola coprocola	79.4397	238	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	-
GCF_000187895.1	s__Phocaeicola plebeius	79.3694	221	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_003437535.1	s__Phocaeicola plebeius_A	79.1701	223	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_013618865.1	s__Phocaeicola sp900541515	79.093	218	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCF_016900355.1	s__Phocaeicola sp900551065	79.0751	205	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	78.9937	195	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCF_900128495.1	s__Phocaeicola ilei	78.8386	182	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCF_000157915.1	s__Phocaeicola coprophilus	78.7271	184	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCA_000432735.1	s__Phocaeicola sp000432735	78.6755	235	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCF_016902295.1	s__Phocaeicola caecigallinarum_A	78.6456	188	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.48	97.48	0.83	0.83	2	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	78.508	218	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCA_900542985.1	s__Phocaeicola sp900542985	78.4462	185	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCA_900552075.1	s__Phocaeicola sp900552075	78.3106	154	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436795.1	s__Phocaeicola sp000436795	78.0156	197	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCF_004793475.1	s__Bacteroides sp002491635	77.3656	110	1090	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
--------------------------------------------------------------------------------
[2023-06-05 08:21:42,615] [INFO] GTDB search result was written to GCA_934692435.1_ERR7747782_bin.13_genomic.fna/result_gtdb.tsv
[2023-06-05 08:21:42,615] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:21:42,619] [INFO] DFAST_QC result json was written to GCA_934692435.1_ERR7747782_bin.13_genomic.fna/dqc_result.json
[2023-06-05 08:21:42,619] [INFO] DFAST_QC completed!
[2023-06-05 08:21:42,619] [INFO] Total running time: 0h1m28s