[2023-06-28 23:44:48,427] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:44:48,429] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:44:48,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e629d6d-19e6-436c-b8ac-fa3cb8f0aad4/dqc_reference
[2023-06-28 23:44:49,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:44:49,692] [INFO] Task started: Prodigal
[2023-06-28 23:44:49,692] [INFO] Running command: gunzip -c /var/lib/cwl/stgf22cf38f-ae60-437b-9006-00b7af227768/GCA_020025415.1_ASM2002541v1_genomic.fna.gz | prodigal -d GCA_020025415.1_ASM2002541v1_genomic.fna/cds.fna -a GCA_020025415.1_ASM2002541v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:44:52,962] [INFO] Task succeeded: Prodigal
[2023-06-28 23:44:52,962] [INFO] Task started: HMMsearch
[2023-06-28 23:44:52,963] [INFO] Running command: hmmsearch --tblout GCA_020025415.1_ASM2002541v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e629d6d-19e6-436c-b8ac-fa3cb8f0aad4/dqc_reference/reference_markers.hmm GCA_020025415.1_ASM2002541v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:44:53,214] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:44:53,215] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf22cf38f-ae60-437b-9006-00b7af227768/GCA_020025415.1_ASM2002541v1_genomic.fna.gz]
[2023-06-28 23:44:53,242] [INFO] Query marker FASTA was written to GCA_020025415.1_ASM2002541v1_genomic.fna/markers.fasta
[2023-06-28 23:44:53,242] [INFO] Task started: Blastn
[2023-06-28 23:44:53,242] [INFO] Running command: blastn -query GCA_020025415.1_ASM2002541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e629d6d-19e6-436c-b8ac-fa3cb8f0aad4/dqc_reference/reference_markers.fasta -out GCA_020025415.1_ASM2002541v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:44:53,992] [INFO] Task succeeded: Blastn
[2023-06-28 23:44:53,997] [INFO] Selected 13 target genomes.
[2023-06-28 23:44:53,997] [INFO] Target genome list was writen to GCA_020025415.1_ASM2002541v1_genomic.fna/target_genomes.txt
[2023-06-28 23:44:53,998] [INFO] Task started: fastANI
[2023-06-28 23:44:53,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22cf38f-ae60-437b-9006-00b7af227768/GCA_020025415.1_ASM2002541v1_genomic.fna.gz --refList GCA_020025415.1_ASM2002541v1_genomic.fna/target_genomes.txt --output GCA_020025415.1_ASM2002541v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:45:00,014] [INFO] Task succeeded: fastANI
[2023-06-28 23:45:00,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e629d6d-19e6-436c-b8ac-fa3cb8f0aad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:45:00,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e629d6d-19e6-436c-b8ac-fa3cb8f0aad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:45:00,027] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:45:00,027] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:45:00,027] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	79.788	198	347	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	78.6549	135	347	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.5443	146	347	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	77.7892	121	347	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.7063	86	347	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.6181	110	347	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.568	98	347	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.5149	105	347	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.3251	94	347	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.2139	66	347	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	77.1046	68	347	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:45:00,029] [INFO] DFAST Taxonomy check result was written to GCA_020025415.1_ASM2002541v1_genomic.fna/tc_result.tsv
[2023-06-28 23:45:00,030] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:45:00,030] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:45:00,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e629d6d-19e6-436c-b8ac-fa3cb8f0aad4/dqc_reference/checkm_data
[2023-06-28 23:45:00,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:45:00,055] [INFO] Task started: CheckM
[2023-06-28 23:45:00,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020025415.1_ASM2002541v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020025415.1_ASM2002541v1_genomic.fna/checkm_input GCA_020025415.1_ASM2002541v1_genomic.fna/checkm_result
[2023-06-28 23:45:17,409] [INFO] Task succeeded: CheckM
[2023-06-28 23:45:17,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:45:17,436] [INFO] ===== Completeness check finished =====
[2023-06-28 23:45:17,436] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:45:17,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020025415.1_ASM2002541v1_genomic.fna/markers.fasta)
[2023-06-28 23:45:17,437] [INFO] Task started: Blastn
[2023-06-28 23:45:17,437] [INFO] Running command: blastn -query GCA_020025415.1_ASM2002541v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e629d6d-19e6-436c-b8ac-fa3cb8f0aad4/dqc_reference/reference_markers_gtdb.fasta -out GCA_020025415.1_ASM2002541v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:45:18,666] [INFO] Task succeeded: Blastn
[2023-06-28 23:45:18,670] [INFO] Selected 22 target genomes.
[2023-06-28 23:45:18,670] [INFO] Target genome list was writen to GCA_020025415.1_ASM2002541v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:45:18,690] [INFO] Task started: fastANI
[2023-06-28 23:45:18,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgf22cf38f-ae60-437b-9006-00b7af227768/GCA_020025415.1_ASM2002541v1_genomic.fna.gz --refList GCA_020025415.1_ASM2002541v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020025415.1_ASM2002541v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:45:29,103] [INFO] Task succeeded: fastANI
[2023-06-28 23:45:29,133] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:45:29,133] [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_018228705.1	s__Dysosmobacter sp018228705	80.4706	225	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	80.4145	211	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCA_019118505.1	s__Dysosmobacter excrementavium	80.176	196	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118935.1	s__Dysosmobacter pullicola	80.1201	203	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	80.1161	205	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544955.1	s__Dysosmobacter sp900544955	79.9433	199	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	79.9427	193	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558115.1	s__Dysosmobacter sp004558115	79.9	149	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005121165.2	s__Dysosmobacter welbionis	79.7547	200	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.82	98.27	0.84	0.73	10	-
GCA_017469475.1	s__Dysosmobacter sp017469475	79.5307	160	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	97.68	97.62	0.84	0.82	4	-
GCA_017937405.1	s__Dysosmobacter sp017937405	79.2786	171	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403435.2	s__Dysosmobacter sp000403435	79.1431	181	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.32	98.32	0.80	0.80	2	-
GCA_016293265.1	s__Dysosmobacter sp016293265	78.7929	151	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584075.1	s__Dysosmobacter sp910584075	78.6945	170	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017482345.1	s__Dysosmobacter sp017482345	78.6032	111	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161215.1	s__Flavonifractor avistercoris	78.4583	123	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_014334055.1	s__NSJ-62 sp014334055	78.3681	163	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900763685.1	s__Dysosmobacter sp900763685	78.2904	120	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159265.1	s__Flavonifractor sp002159265	77.8939	114	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811815.1	s__Flavonifractor sp017811815	77.8796	99	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161085.1	s__Flavonifractor avicola	77.7474	99	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.94	96.68	0.83	0.78	7	-
GCF_900626145.1	s__Intestinimonas timonensis	77.6727	109	347	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:45:29,135] [INFO] GTDB search result was written to GCA_020025415.1_ASM2002541v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:45:29,136] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:45:29,140] [INFO] DFAST_QC result json was written to GCA_020025415.1_ASM2002541v1_genomic.fna/dqc_result.json
[2023-06-28 23:45:29,141] [INFO] DFAST_QC completed!
[2023-06-28 23:45:29,141] [INFO] Total running time: 0h0m41s